Cydia stuck on "Preparing Filesystem"

After using jbme.com and seeing how unstable it was, I used redsn0w to jailbreak my phone. Everything went smoothly, but it deleted all of the jailbreak apps. Oddly enough, the tweaks and themes were still active.

Winterboard was still accessible via Settings, but the app was gone. SBSettings no longer worked, as when I would swipe down from the status bar, I would get a message saying "It is potentially dangerous to perform actions while Cydia is installing software." from Activator.

I would do a reset, but it would boot in Safe Mode, in which Cydia would still say "Preparing Filesystem". Swiping down for SBSettings tells me it's in Safe Mode, so I restart SB from the message it gives me. It would restart into normal mode.

Cydia will try to "prepare the filesystem" once more, restarting the phone again, but going back to the Cydia app brings up the "Preparing Filesystem" mesage again and results into another reset (I'm typing as I do all of this).

I MRoogled and Googled and found no one mentioning this message coming up. Anyone have this experience happen and know of the best solution? I'd like to actually be able to modify and add apps again from Cydia.

It wouldn't have something to do with installing the multitasking gestures, would it? I told redsn0w to do that and it's in Settings now and working.

In case anyone else encounters the same problem, I had to restore on iTunes, performed a backup, then rejailbroke my iPhone. Having some issues with the jailbreak, but none that is causing this problem.