I finally upgraded to 3.55 after hanging at 3.41 for awhile. I thought this would fix my problem with GT5 never loading but even with the new 3.55 CFW Kwameand the original eboot and param.sfo and having the gamedata deleted the game would still freeze in the normal spot. I was also having problems with ACB loading though it worked fine before with clean eboots.
My fix was simply to reformat the HDD. Once I did that, and reinstalled all my managers/lvl2 patch/fix permissions, GT5 worked clean no changes updated to the latest patch, ACB worked fine no changes on the latest patch, all my old games work that worked before, external and internal, and all 3.50 games I have tested boot fine and clean (DBZ:RB2, Splatterhouse, Two Worlds).
All the games that worked on 3.41 work still, and all the new problematic 3.50 games work clean now. I have no had any issues since I decided to reformat the internal HDD.
I would think this is obvious, but I will warn you guys anyway. Formatting the HDD erases ALL DATA ON THE HDD, AND YOU CANNOT GET IT BACK. Makre sure you back up all your game saves, and back up your internal games if necessary (I just reripped mine from my blu-rays).
So if your pulling your hair trying to get a game to work give this a try, it fixed all of my problems. I was reluctant to do it at first, but I had to give GT5 1 more shot before I gave up, backed up all my games, epic success.