****UPDATE!*** 2/14/2014
I'm WAY over due for this, but I got it working a few days after posting this problem. Since posting this, I've had numerous people messaging me about this same issue, asking for help. I got lucky with this fix all because of a second PS3 I own. So if you happen to have one too, then keep reading: What I did was I made a new user account WITHOUT signing in my PSN info. I instead immediately fired up the game, earned those trophies, and then signed in to PSN, and synced the trophies to the account. This took them out of the bubble.
If you don't have a second PS3 this other probable fix is annoying, but it will more than likely do the trick. Basically you're going to have to back up your most important game save files on your system (to PS+ or flashdrive), and restore it to factory settings. This will wipe things clean and you can do the above mentioned fix from there. Good luck and my apologies for not saying this when I fixed it initially, lol.
- that2009chick
