I had a problem where GT5 had stopped loading for me at all, while all other games worked. What I had to do to fix this is as fallows. If you want to keep your save files back them up first! Wipe the entire HDD, Install only Gaia Manager latest version, and Open manager's latest version.
Run Gaia Manager with GT5 disc in the drive, make sure Memory patch is selected before copying the game over! Then dump GT5 to your internal drive again. Replace Eboot.bin as you normally would, skip updates..
Should work fine, I think my problem was I had too many loaders, and the param.sfo files kept getting edited/ unedited making GT5 not work if that makes sense..
Hope this helps. PS3 fat, 3.41 Jailbroken, Hermes4b, spoofed to 3.55 (don't think that matters though) I always run games with a Game disc in the drive for compatibility.