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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

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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.

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Strangely enough, I suspected the same thing and just 30 minutes ago I did that exactly that, but I didn't delete all preferences - only the jailbreaks that I no longer use, and it didn't have any affect. I did also plan to try Twitter before I squirted (excuse the terminology - I picked it up from the guys I worked with. It's what they refer to as "restoring an image") the backup back on, but the iOS 5 setup screen asked if I wanted to restore from a backup and I just went along with it. :L I'll try your advice and get back to you. Thanks! –  mythofechelon Feb 7 '12 at 10:43
    
Deleting all ".plist"s in "Library\Preferences\SystemConfiguration" and rebooting didn't work. Deleted all ".plist"s in "var\mobile\Library\Preferences" and rebooting resulted in it starting in iOS 5's "first setup mode" with all my data and system settings set and the jailbreak's present and working (some blank or set to default, due to the missing preference files), which was really bizarre. But yeah, Twitter still crashed in the app and in Settings. :( –  mythofechelon Feb 7 '12 at 15:39
    
@BenHooper You are searching for a needle in a haystack here. Honestly, I think the best solution is to put the device in DFU mode, set it up as a new phone, ensure things are working, and then manually installing all your apps again. From there, you can jailbreak and restore the data to each specific app (most probably won't need a restore, perhaps only games with saved progress) and start fresh. This will ensure the cleanest working environment possible and is much simpler than digging around thousands of config/system files, deleting blindly. –  cksum Feb 7 '12 at 20:29
    
Not being able to use the official Twitter App isn't worth losing 3 years of text messages, notes, etc and having to set all of my preferences again. I'll just hope that a future iOS and/or Twitter update will undo this glitch. I can cope with mobile.twitter.com for now. Thanks anyway. –  mythofechelon Feb 7 '12 at 23:12
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