I've had the same issue with apps disappearing. It appears to be ones that I've moved to the media area. Since I stopped moving apps to the media area, I haven't noticed any more apps disappearing. Hopefully this is will be fixed!
My question is, what is the media area? Is it on the phone or on the sdcard? What is it's purpose?
The Bionic has 2 SD cards. One built inside the phone and one you can grab. They've renamed it to "Media Area" for some reason.