Steps to reproduce on Windows:
1 > del %USERPROFILE%\.jedit\recent.xml %USERPROFILE%\.jedit\perspective.xml
2 > jedit.exe SubmitChecks.pl file2
3 When jEdit window opens, choose File --> Exit
4 > jedit.exe
5 When jEdit window reopens, you see a 'phantom' buffer with the path of SubmitChecks.pl file, but no content.
The problem is related to perspective.xml, I think.
I also believe this bug was not in jEdit 4.3, but I'm not sure about this.
jEdit 4.4 server mode, using Sun Java 1.6.0_23, Win 7 64-bit, All plugins disabled
Possibly relevant setting: Global Options --> jEdit --> General --> Restore previously open files on startup is NOT checked.