A buddy turned me onto this program, and I have the same issue, however, relaunching the software does not fix it. The old entries stay in the par2 tab and when i try to delete they just gray out and stay put. Cleanup does nothing.
I have noticed it still unrars, but it will not auto-delete the .rar files when its finished. Hope this helps, I can take some screens if you think it will help.
Keep up the good work ,this program is excellent.