I don't have the same issue, but I have a similar one:
I just jailbroke using limera1n and everything went perfect, but I get the same message when opening Cydia for the first time (Reorganizing... Will automatically close when done)... it just doesn't do anything after that. I've kept my phone from sleeping for over 10 minutes, and it still says that... and when I go home, all my icons are still there, but when I go back to Cydia it's just the same thing. The couple of times when I waited long enough for the message to go away and the phone to reload by itself, when I go back to Cydia I STILL get the same message. 😕
I've rebooted my phone. The one thing I'm trying to avoid is restoring and then rejailbreaking, but I'll do it if I have to. I'm just wondering if maybe there's another way, like reinstalling Cydia or something?