There are quite a few bugs on Fat Jar Tracker lately, some of them related to incompatibility with Eclipse 3.3 release (aka. Europa). It's been a long time since I touched the code-base of Fat Jar plug-in, There were several Eclipse 3.3 API incompatibilities including setSorter(ResourceSorter rs) method, now deprecated, and replaced with setSorter(ResourceComparator rc) in org.eclipse.ui.dialogs.ElementTreeSelectionDialog class etc. I'm glad to have no other major, and painful, changes :) (at least, I haven't encounter one so far).
If you are code freak, changes are committed to cvs repository at fjep.cvs.sf.net. For the users, Since I'm just a developer member of the project, I don't have enough rights to upload the build and release the plug in officially, all I can do is to provide you a link for the latest build which works with Europa release. As of this time, I'm not sure when the latest plug in will be available from sf.net, in the mean time you can download it from here.
Enjoy Deployment with Europa :)!