This is more an annoyance report than a request for help; I doubt if there's anything that can be done.
I've got a Samsung Stratosphere with Android Gingerbread. I've recently done some organizing, and created a folder on one of the home screens for favorite apps. I moved 9 app shortcuts there. Today when I restarted my phone trying to solve another problem, I found that the system had duplicated all the shortcuts in this folder: every shortcut was in there twice, and I had to delete them manually. Later when I restarted again, I found that all but 3 of the shortcuts had been removed from the folder entirely! I had to recreate them.
I also use folders to organize apps in the app drawer (or whatever it's called when you tap Applications from the home screen). I find that fairly often one or two apps have "escaped" from their folders, generally always the same one or two. I put them in and a day or two later they're out again.
None of this is a major issue, just a stupid, stupid annoyance that a well-functioning operating system ought not to have. I am a little curious whether anyone else has had them.