Why does iOS remove aps from folders upon update?
I've seen similar issues on both my iPad and iPhone, so it is possible they may be in some way related, though my problem can occur with one app update or many.

I run into apps jumping out of their folders most when one app in particular has problems downloading or installing. (For example, I will often see an app in a perpetually installing state.) The only way to fix this reliably is to Respring or reboot, and that's when my apps jump out of their folders.

I'm not sure it has anything to do with being jailbroken, because I have seen similar behavior on my iDevices when I couldn't jailbreak them (though not as often). I suspect when an install or download goes awry and Springboard is restarted, it simply resets things on that app and treats it like a new install (which would explain why mine always end up after all the other icons and never intermixed). 

A similar phenomenon is purely jailbreak related. If you have folder enhancers on your device (say, Infinifolder), and your device has to go to Safe Mode (or something else freaky happens), iOS puts the apps into a very funny order, and often out of folders. I think this is because the folder enhancers don't quite correctly keep iOS's own map of where things are up-to-date (and can't in some cases, especially if you have a folder in a folder or more than 12 or so apps in a folder), and iOS has to figure out somewhere to put them.

Definitely weird, odd, and even annoying (especially when all your apps jump folders and your well-ordered screens have to be rebuilt. sigh.)