I had a sililar issue but respringing fixed it. How do we dont what app is starting up and doing this? I made sure to only insta; IPAD tweeks....On my IPAD 3, it only seems to happen if I turn off the ipad and then turn it back on.... I dont do that too much... as I said, after I turn it back on a resapring fixes it
Unfortunately, it still is because of an incompatible tweak. It doesn't whether it's incompatible because your iPad's not a phone or the iOS is new, that type of behavior is going to happen because a malfunctioning tweak is causing it.
I know this personally because I just got done with a long session of trying to figure out the very problem you had (after turning off, then on - or re-booting my iPad3, I had to respring to get my it to look right). It was driving me nuts because I couldn't figure it out - and I really didn't want to remove any of the tweaks I had. I have so few and they are what I wanted!
But, I bit the bullet and determined that i had to remove the tweak Move2Unlock. Don't you know that hurt my feelings ... bad! However, I've almost convinced myself that I LIKE "slide to unlock" actions.
But enough about me...
The gist of this is that you have a misbehaving tweak, whether you think so or not. You'll have to go through them, one-by-one until you find the one that's misbehaving. Or, don't turn off/on (or reboot) the iPad. Those are really the only two options. Sorry.
Marilyn