there are none - actually running a .war with gemjar might have issues on some servers (esp. if they do not expand the deployed .war, since then it's quite hard to reference files/resources packaged in a .war while still inside a .jar). on the other hand it should roll fine if things are expanded (even with gemjar) ...
you should definitely report this with Warbler's repository (if not reported already).
it should not be hard to fix - likely a one liner, I know a PR would be most welcome :)
NOTE: on the other hand if it worked in a previous JRuby and updating 1.7.x is the issue, than it might be a "regression" on JRuby's side and they might actually fix this if they knew about it ...