We solved this, for the record here is the cause:
Our 2 .war files were named according to this convention:
Ourproject.pkg.war.file1.war
Ourproject.pkg.war.file2.war
We solved the issue by renaming them in this convention:
Ourproject.pkg.web.file1.war
Ourproject.pkg.web.file2.war
It seems that the deployer parses the .war file name in the web-uri of the application.xml, it stops at the first occurrence of the word ".war" and uses that name.
Hence following our initial convention, both .wars would have been deemed "the same".
Simply renaming them and adjusting the corresponding config files fixed it!
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