When I run jedit foo.bar I'd expect jedit to open the file "foo.bar" in the *CURRENT* directory. That's not what happens - instead, jedit tries to open a file in the /usr/share/jedit directory. . That does not seem to be a problem of jedit per se, as java -jar /usr/share/jedit/jedit.jar foo.bar works as expected. The issue also appears, when I use a relative path specification (e.g. "jedit ../blah/blah.txt"). This happens with Sun JRE 1.6 and also IBM JRE 1.6.
Fixed in 4.3_pre13.