Several package scanner warning messages in jira 4.0.1 logs

After upgrading to Jira 4.0.1 I see a LOT of these warning messages in my logs. So far these warnings do not appear to be harmful, but please confirm.. and is there anyway to get around them??

I am copying 'few' lines here.

Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.xml.namespace' with different versions. Files: stax-api-1.0.1.jar and axis-jaxrpc-1.3.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.factory' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.extensions.http' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.extensions.soap' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.extensions.schema' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.extensions.mime' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.xml' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.wsdl.extensions' with different versions. Files: wsdl4j-1.6.1.jar and axis-wsdl4j-1.5.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.xml.namespace' with different versions. Files: xml-apis-1.3.04.jar and stax-api-1.0.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'javax.xml' with different versions. Files: xml-apis-1.3.04.jar and stax-api-1.0.1.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.catalina.startup' with different versions. Files: tomcat-i18n-en.jar and bootstrap.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.catalina.loader' with different versions. Files: tomcat-i18n-en.jar and bootstrap.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.catalina.security' with different versions. Files: tomcat-i18n-en.jar and bootstrap.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.naming' with different versions. Files: tomcat-i18n-en.jar and bootstrap.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.catalina.security' with different versions. Files: tomcat-i18n-es.jar and tomcat-i18n-en.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.tomcat.util.http.res' with different versions. Files: tomcat-i18n-es.jar and tomcat-i18n-en.jar
Dec 23, 2009 11:01:58 AM org.twdata.pkgscanner.ExportPackageListBuilder logDuplicateWarning
WARNING: Package Scanner found duplicates for package 'org.apache.catalina.connector' with different versions. Files: tomcat-i18n-es.jar and tomcat-i18n-en.jar

—
Here is my environment

___ Environment ___________________

JIRA Build : 4.0.1#471
Build Date : Fri Nov 27 00:00:00 EST 2009
JIRA Installation Type : EAR/WAR
Application Server : Apache Tomcat/5.5.27 - Servlet API 2.4
Java Version : 1.6.0_17 - Apple Inc.
Current Working Directory : /usr/local/apache-tomcat-5.5.27/logs
Maximum Allowable Memory : 1894MB
Total Memory : 354MB
Free Memory : 105MB
Used Memory : 249MB
Memory Pool: Code Cache : Code Cache: init = 2560000(2500K) used = 8662016(8459K) committed = 8785920(8580K) max = 67108864(65536K)
Memory Pool: Par Eden Space : Par Eden Space: init = 16384000(16000K) used = 15815144(15444K) committed = 16384000(16000K) max = 32702464(31936K)
Memory Pool: Par Survivor Space : Par Survivor Space: init = 2686976(2624K) used = 782560(764K) committed = 2686976(2624K) max = 5439488(5312K)
Memory Pool: CMS Old Gen : CMS Old Gen: init = 246677504(240896K) used = 245532360(239777K) committed = 353013760(344740K) max = 1948712960(1903040K)
Memory Pool: CMS Perm Gen : CMS Perm Gen: init = 134217728(131072K) used = 97739256(95448K) committed = 143368192(140008K) max = 268435456(262144K)
JVM Input Arguments : -Djava.util.logging.config.file=/usr/local/apache-tomcat-5.5.27/conf/logging.properties -XX:PermSize=128m -XX:MaxPermSize=256m -XX:ReservedCodeCacheSize=64m -Xms256m -Xmx1900m -Djava.awt.headless=true -Dcom.sun.management.jmxremote.port=8055 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.password.file=/Users/bandlamudib/.jmxremote.password -Dorg.apache.catalina.session.StandardSession.ACTIVITY_CHECK=true -Datlassian.mail.senddisabled=true -Datlassian.mail.popdisabled=true -Dapproval.mail.disabled=true -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dconfluence.disable.peopledirectory.anonymous=true -Dmail.mime.decodeparameters=true -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xdebug -Xrunjdwp:transport=dt_socket,address=9777,server=y,suspend=n -Djava.endorsed.dirs=/usr/local/apache-tomcat-5.5.27/common/endorsed -Dcatalina.base=/usr/local/apache-tomcat-5.5.27 -Dcatalina.home=/usr/local/apache-tomcat-5.5.27 -Djava.io.tmpdir=/usr/local/apache-tomcat-5.5.27/temp

___ Java System Properties _______

apple.lang.DisableCompatibilityClasspath : true
approval.mail.disabled : true
atlassian.mail.popdisabled : true
atlassian.mail.senddisabled : true
awt.nativeDoubleBuffering : true
awt.toolkit : apple.awt.CToolkit
catalina.base : /usr/local/apache-tomcat-5.5.27
catalina.home : /usr/local/apache-tomcat-5.5.27
catalina.useNaming : true
com.sun.management.jmxremote.password.file : /Users/xxxxxxxxxxxxx/.jmxremote.password
com.sun.management.jmxremote.port : 8055
com.sun.management.jmxremote.ssl : false
common.loader : ${catalina.home}/common/classes,
${catalina.home}/common/i18n/*.jar,
${catalina.home}/common/endorsed/*.jar,
${catalina.home}/common/lib/*.jar
confluence.disable.peopledirectory.anonymous : true
file.encoding : MacRoman
file.encoding.pkg : sun.io
ftp.nonProxyHosts : local|.local|xxxxxxx.xxxxxxx/16
gopherProxySet : false
http.nonProxyHosts : local|*.local|xxxxxxxx4/xxxxxxxx/16
java.awt.graphicsenv : apple.awt.CGraphicsEnvironment
java.awt.headless : true
java.awt.printerjob : apple.awt.CPrinterJob
java.class.version : 50.0
java.home : /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
java.io.tmpdir : /usr/local/apache-tomcat-5.5.27/temp
java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory
java.naming.factory.url.pkgs : org.apache.naming
java.rmi.server.randomIDs : true
java.runtime.name : Java(TM) SE Runtime Environment
java.runtime.version : 1.6.0_17-b04-248-10M3025
java.specification.name : Java Platform API Specification
java.specification.vendor : Sun Microsystems Inc.
java.specification.version : 1.6
java.util.logging.config.file : /usr/local/apache-tomcat-5.5.27/conf/logging.properties
java.util.logging.manager : org.apache.juli.ClassLoaderLogManager
java.vendor : Apple Inc.
java.vendor.url : http://www.apple.com/
java.vendor.url.bug : http://bugreport.apple.com/
java.version : 1.6.0_17
java.vm.info : mixed mode
java.vm.name : Java HotSpot(TM) 64-Bit Server VM
java.vm.specification.name : Java Virtual Machine Specification
java.vm.specification.vendor : Sun Microsystems Inc.
java.vm.specification.version : 1.0
java.vm.vendor : Apple Inc.
java.vm.version : 14.3-b01-101
mail.mime.decodeparameters : true
mrj.build : 10M3025
mrj.version : 1060.1.6.0_17-248
org.apache.catalina.session.StandardSession.ACTIVITY_CHECK : true
org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true
os.arch : x86_64
os.name : Mac OS X
os.version : 10.6.2
package.access : sun.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.tomcat.,
org.apache.jasper.,
sun.beans.
package.definition : sun.,
java.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.tomcat.,
org.apache.jasper.
server.loader : ${catalina.home}/server/classes,
${catalina.home}/server/lib/*.jar
shared.loader : ${catalina.base}/shared/classes,
${catalina.base}/shared/lib/*.jar
socksNonProxyHosts : local|*.local|xxxxxxx/xxxxxxx/16
sun.arch.data.model : 64
sun.boot.library.path : /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries
sun.cpu.endian : little
sun.cpu.isalist :
sun.io.unicode.encoding : UnicodeLittle
sun.java.launcher : SUN_STANDARD
sun.jnu.encoding : MacRoman
sun.management.compiler : HotSpot 64-Bit Server Compiler
sun.os.patch.level : unknown
tomcat.util.buf.StringCache.byte.enabled : true
user.country : US
user.dir : /usr/local/apache-tomcat-5.5.27/logs
user.home : /Users/xxxxxxxx
user.language : en
user.name : xxxxxxxxx
user.timezone : America/New_York
vendor : Apache Software Foundation
vendor-url : http://xml.apache.org/xalan-j
version : 1.0

2009-12-23 11:01:47,043 main INFO [atlassian.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2009-12-23 11:01:51,074 main INFO [atlassian.jira.startup.CompositeJiraHomePathLocator] jira.home '/data0/jira-data' found using Application Properties.
2009-12-23 11:01:51,103 main INFO [atlassian.jira.startup.JiraHomeStartupCheck] The jira.home directory '/data0/jira-data' is validated and locked for exclusive use by this instance.
2009-12-23 11:01:51,103 main INFO [atlassian.jira.startup.JiraStartupLogger] JIRA startup checks completed successfully.
2009-12-23 11:01:51,105 main INFO [atlassian.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration _______

Loading entityengine.xml from : file:/usr/local/apache-tomcat-5.5.27/webapps/helpdesk/WEB-INF/classes/entityengine.xml
Entity model data source name : defaultDS
Entity model field type name : mysql
Entity model schema name :
Database Version : MySQL - 5.1.31
Database Driver : MySQL-AB JDBC Driver - mysql-connector-java-5.1.7 ( Revision: ${svn.Revision} )
Database URL : jdbc:mysql://xxxxx.xxxxxx.xxxx/xxxxxxxxxx?autoReconnect=true
Database JNDI address : java:comp/env/jdbc/JiraDS