I think I figured it out. Did everyone, by any chance, have their device previously jailbroken? Then when they backed up their apps with iCloud, iCloud saved them? Then when trying to restore to a previous backup after upgrading to IOS6 all the apps showed up but just say waiting underneath? Well the reason it keeps asking for the apple id and password is because of those apps. As I noticed, the apps that are like that, when I tap on them the same window shows up asking for my info. All I did was erase the apps that were 'waiting' that were previously downloaded from when my iPad was jailbroken and I haven't gotten the little pop up since, its associated with the apps, I noticed that, but not exactly what its reasoning behind it is, probably because it is asking for your ID in order to download it, but when it can't connect, because of it being a pirated app, the device gets confused and when isn't able to download the first time, it will try again and continuously ask for your ID in order to confirm its download.
Hope this helps.
- After this upgrade I'm going to be avoiding jailbreaking and just deal with what I have to app wise.