Confluence 5.6.6 Windows Installer is not properly detecting modifications

There's list of modifications to determine which files we need to backup and possibly restore afterward. The file list is incorrect:

Here's the output of the modifications of Confluence 5.5.1

The following provides a list of file modifications within the confluence directory.

Modified files:
confluence\WEB-INF\web.xml
jre\lib\security\cacerts
conf\server.xml
Removed files:
(none)
Added files:
confluence\WEB-INF\lib\mysql-connector-java-5.1.11.jar
bin\ntlmauth.dll
bin\sqljdbc_auth.dll
lib\sqljdbc4.jar

Here is from 5.6.3:

The following provides a list of file modifications within the confluence directory.

Modified files:
confluence\WEB-INF\web.xml
Removed files:
(none)
Added files:
confluence\WEB-INF\lib\mysql-connector-java-5.1.11.jar