I've got this same issue too. And now that iOS 6.1.3 is out (and the signing window for iOS 6.1.2 is closed) we don't really have the option to "restore to fix it for awhile, until it inexplicably returns." That sucks.
So now I am uninstalling tweaks one-by-one to try and figure out the culprit, and nothing appears to be helping. My pet theory right now is that some popular tweak we install has some dependency installed along with it, and uninstalling via Cydia doesn't remove it; that dependency is left behind as cruft. And that's what's causing the issue.
I do hope we're able to definitively figure out what's causing it, because it sure is annoying, and then perhaps the developer responsible for the code behind it can fix it.