Depending on when XWiki.getWorkDirectory() is first called, the core may chose a different work directory.

To repeat:
Switch on filesystem attachment storage.
Start XWiki,
call XWiki.getWorkDirectory()
note it is something like:
/var/log/tomcat/work
disable filesystem attachments,
restart and call again,
note it is something like:
/usr/share/tomcat5.5/work/Catalina/localhost/xwikiTrunk

filesystem attachments is called in the construction of the XWiki object and in one of it's initialize() functions, it calls XWiki.getWorkDirectory(). This should be okay but apparently tomcat changes the home directory after the servlet is brought up. Since the file from the first call is stored, the same file is returned until the wiki is restarted.