So glad I found this thread... I was starting to think I was the only one on the planet having this issue. Just wanted to add my experience so far & any information I can. There is 0 doubt in my head at this point that the issue stems from the Mobilesubstrate update that was released with the Winterboard update. I started having issues immediately on an iPhone 5 running 6.1 at the time (Running 6.1.2 now) on AT&T. I had 0 issues whatsoever before that update. I had just got my iPhone 5 & was thrilled with how well everything was running. I literally had 0 crashes. The update immediately made my home button slow to respond, the slider slow, scrolling slow, app crashes, especially Settings & Cydia, etc. Steps I have taken since then include:
1. Disabling all themes, helped a little, but not much.
2. Downgrading Winterboard, did not help.
3. Downgrading Mobilesubstrate, did not help.
4. Deleting Winterboard, immediately solved the problem. Though I am pretty convinced the issue is Mobilesubstrate's interaction with it.
5. Numerous full restores, reset all settings, restore from backup. Never solved the problem. Probably did no less than 5 of these.
6. Finally copied all my relevant app data & did a clean install without a restore from backup & was convinced this was the massive pain in the butt that would solve the problem. In some ways it did. Response time is back to normal. Settings & Cydia rarely crash, but lots of iOS apps do. Facebook, Instagram, Flipboard, Podcasts, etc. Once an app starts crashing it will not stop without a restart.
So, this is where I sit. Literally countless hours of trying to solve this problem. So, here is hoping this issue gets solved sometime soon. At the moment my only course of action is removing Winterboard which does solve the problem. I'm trying a downgrade of Mobilesubstrate, Winterboard, & Safesubstrate right now on my fresh install to see if it helps. It didn't previously!
Here is a syslog of a Facebook crash:
http://pastie.org/6338798
Update: Downgrading didn't help!