Same here. I actually installed a bunch of stuff on Cydia at once, including Backgrounder, and when I rebooted, I kept going into Safe Mode. Ended up having to remove all my Cydia apps and then reinstall them one-by-one to find the culprit.
I've also noticed that iBooks crashes upon launch, the new Apple app "Trailers" (for movie info) crashes when you click on certain functions, and Cydia crashes randomly. The Location toggle under SBSettings doesn't work, and some of the toggles (like 3G, data, wifi, bluetooth- stuff I don't care for) can't be removed from the notification menu. Running iPhone 4, iOS 5, tethered JB with redsn0w b5.
Oh yeah, and Winterboard doesn't work either for me.