I have a simple test.xml file committed to a repository:

<?xml version="1.0"?>
<project name="test" default="" basedir=".">

  <target name="test-arg-with-comma">
    
    <echo>Ant arg received: ${arg.with.comma} </echo>
  
  </target>

</project>

I configured an Ant task in a Bamboo plan this way:

• Build file: test.xml
• Target: test-arg-with-comma -Darg.with.comma=\"arg1 with comma, arg2 with comma\"
• The build is successful, but this is the log output relevant to the Ant task:

  13-Jun-2012 18:05:51	Starting task 'My Ant Task' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
  13-Jun-2012 18:05:51	
  Beginning to execute external process for build 'My Project - Ant Test Plan - Default Job'
   ... running command line: 
  C:\Atlassian\apache-ant-1.8.3\bin\ant.bat
    -Djava.io.tmpdir=C:\Windows\Temp\MPR-ATP-JOB1
    -f
    test.xml
    test-arg-with-comma
    -Darg.with.comma=\"arg1 with comma, arg2 with comma\"
   ... in: C:\Atlassian\atlassian-bamboo-4.0.1\Bamboo\bamboo_home\xml-data\build-dir\MPR-ATP-JOB1
   ... using extra environment variables: 
  JAVA_HOME=C:\Program Files\Java\jdk1.6.0_23
  ANT_HOME=C:\Atlassian\apache-ant-1.8.3
  Path=C:\Program Files\Java\jdk1.6.0_23\bin;C:\Program Files\Java\jdk1.6.0_23\bin;C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;c:\Program Files\WIDCOMM\Bluetooth Software\;C:\Program Files\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\Wave Systems Corp\Gemalto\Access Client\v5\;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Program Files\Common Files\Roxio Shared\OEM\DLLShared\;C:\Program Files\Common Files\Roxio Shared\OEM\DLLShared\;C:\Program Files\Common Files\Roxio Shared\OEM\12.0\DLLShared\;C:\Program Files\Roxio\OEM\AudioCore\;C:\Program Files\Windows Live\Shared;C:\Program Files\TortoiseSVN\bin;C:\Program Files\Subversion\bin;C:\Program Files\Perforce;C:\Perforce;C:\Atlassian\atlassian-plugin-sdk-3.9.2\bin;C:\Program Files\Mercurial\;C:\Program Files\Apache Software Foundation\apache-maven-3.0.4\bin;C:\Perforce\p4;C:\Program Files\cvsnt;C:\Program Files\Git\bin;C:\Program Files\Java\jdk1.6.0_23\bin;C:\Program Files\Apache Software Foundation\apache-maven-3.0.4\bin;C:\Atlassian\apache-ant-1.8.3\bin;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\CVSNT\;C:\Perforce\Server
  13-Jun-2012 18:05:51	Buildfile: C:\Atlassian\atlassian-bamboo-4.0.1\Bamboo\bamboo_home\xml-data\build-dir\MPR-ATP-JOB1\test.xml
  13-Jun-2012 18:05:51	
  13-Jun-2012 18:05:51	test-arg-with-comma:
  13-Jun-2012 18:05:51	     [echo] Ant arg received: "arg1 with comma arg2 with comma" 
  13-Jun-2012 18:05:51	
  13-Jun-2012 18:05:51	BUILD SUCCESSFUL
  13-Jun-2012 18:05:51	Total time: 0 seconds
  13-Jun-2012 18:05:51	Finished task 'My Ant Task'
  

As can be seen, first it recognizes the comma:

  -Darg.with.comma=\"arg1 with comma, arg2 with comma\"

But later on, it's not recognized:

13-Jun-2012 18:05:51	     [echo] Ant arg received: "arg1 with comma arg2 with comma" 

This works if I try on Linux.