i have the same thing, i jailbreaked a ps3 with bad laser (i think) and can play emulators effortless. Only when i try backups it shows black screen right after loading. It's the same for games that need no original disc to load.
Also, games played from original discs only freeze after some time, not instantly like with the jailbreaked games. Untill now i couldn't really find what it was so any help is welcome
Also please, if anyone finds a solution, post it because it probably will help many others ;-)
(it's a older big ps3, don't know if that changes anything at all)
Since i'm not sure it's the laser, when i have the time i will try what pockets69 said (i did format, but not restore settings) on my original hd. (read somewhere similar problems happen with bad sectors on the hard drive).