I think this may be hardware and or software based on what approach apple has taken with their new A6 chip as well as iOS6 (and whether or not I understand this fully) but it may not be the end of the world.
Lets take a step back. As others have mentioned, this is not something that happens all of the time right? And what do we know about the keyboard flicker? Well its very much the artifacting you would expect when you overclock a graphics card on a PC and the chip is at its limit. This cannot be the case here because the A6 will be tested and any falty chips binned. If you go and play the demanding Real Racing 2, do we see artifacting? No, because the chip works fine!
When could we also see artifacting and issues such as the ones we're seeing in the app store keyboard and folders with 4 or more apps? Well if we underclock and undervolt a GPU on a PC enough we could also achieve artifacting and that's where I think the issue lies. I think the clock speeds and voltages are not being managed well or are too agressive and so when the GPU needs to clock up or needs to do more demanding things (at least more demanding than being in standby, the keyboard in the appstore is transparent) the artifacting occurs either because the A6 chip is not reacting quickly enough or again Apple were too agressive in saving power that the standby voltage may be too low. This would explain why if you were to go and play Real Racing 2, close the app and download another you wouldn't encounter this issue because the clock speeds and voltages have been pushed up by Real Racing and will only go down after a period of inactivity (locking). You also wouldn't find this by cold booting your phone because like a PC, clock speeds only fall after there is no activity and there is quite a bit when a phone/PC is booting.
This is may not be 100% the right answer. I might be wrong but seeing as no body knows anything I thought I'd throw this out there.
So Apple would need to find a way by software to sort this (if i'm right) or they can just recall all of their phones...