I don't know what you guy's views on Jailbreaking are, but seeing as it's still an iPhone on an Apple forum.. I know a lot about general problems with iOS and jailbreaking, so this isn't something simple..
I jailbroke my iPhone 4S on the day that the untethered Absinthe jailbreak was released and everything has been working seamlessly for the past couple of weeks, more or less – a few apps wouldn't run, a few white/disappeared/appeared icons here and there, system apps appearing out of nowhere, but nothing that bothered me. But recently I've been having some severe glitches, as follows:
1.) Anything Twitter-related results in a crash – tapping on Twitter in Settings crashes Settings, activating iOS Twitter via Activator crashes Springboard, opening the Twitter app crashes the app. This is the most annoying, as I use Twitter regularly.
2.) Tapping the delete button on any App icon results in a catastrophic crash and Springboard relaunches in MobileSubstrate Safe Mode.
It's logical to think, from the timing, that this is likely caused by a recently-installed tweak, but I don't understand how both things still happen even when in MobileSubstrate SafeMode! Either of these glitches causes the iPhone to restart in SafeMode, which is understandable. But what's even more bizarre is that if I provoke one of these glitches in SafeMode, it resprings in jailbroken mode! What is up with that?!
Has this been happening to anyone else? More importantly, has anyone found a fix? I don't want this to result in the "start from scratch" answer that people are always so eager to dish out unless absolutely necessary. I mean, I have no problem with re-jailbreaking and re-installing the all tweaks, but I have a 64GB iPhone 4S.. Resyncing all that data is going to take a LONG time, and I really don't want to do that unless I HAVE to.
Update:
I reset to factory settings, restored from a backup, reinstalled Twitter and it's STILL happening, even though it's not even jailbroken anymore! Help Q.Q
Best Answer
I'm inclined to think something has corrupted your preference files or application data, as those will be brought back after a restore from backup.
In order to test this theory, you will need to wipe the phone by putting it in DFU mode, then restoring to the latest Apple firmware through iTunes. Then set up your device as a new device. If the problems still occur (unlikely), then I would take it in to an Apple Store and have a Genius look at it.
If, however, it fixes the issue, then you will have to play "hunt and go seek" with the culprit. Restore your backup, jailbreak (but don't install anything from Cydia except OpenSSH so you can access the file system), and root through your "home" folder (/private/var/mobile).
You should try deleting the preferences (plists) first (~/Library/Preferences), then rebooting. Don't worry, iOS will recreate them. If that doesn't fix it, try removing the sqlite database in ~/Library/Twitter, although I have a feeling the preference files should take care of it.
I wish I had an easy answer for you, but it's going to take some study of the file system and tracing back to the package that "infected" your system.
Not everything in Cydia is deemed safe and you may wish to exercise more caution in the future. MobileSubstrate (which is only made possible be reverse engineering) provides the hooks for many deep level APIs that shouldn't be messed with.
Additionally, you may want to hit up jailbreakqa for additional help, as that is the official forum for help on these matters. From my experience, there isn't much help here regarding this process.