Do you mind listing your tweaks if you dont have too many? Maybe this is why you dont any problems
Could it be jelly lock causing issues?
I have 100+ tweaks on my iP4S. So it's not a question of quantity...
The ones affecting the LS (besides Priority Hub) are SubtleLock, 20 Second Lockscreen, SameStatus, StaticLock and BetterPasscodeKeypad.
I don't have (and never had) Jelly Lock. So this one is different to what you have - if it's the culprit I can't say.
Furthermore I don't have any tweaks affecting messages, such as BiteSMS, QR or the like.
Maybe this can help you sort out the problem.