Spent a good few hours at the weekend with my mate trying to fix his problems with Uncharted 3.
I have a PS3 40gb (upgraded to 250GB).
He recently replaced his launch 60GB with a new PS3 Slim 160GB. He reused his 250GB Western Digital drive from his 60GB. I noticed from day 1 it was laggier and would stutter playing back video when downloading.
I he recently had major problems with Uncharted 3. They ranged from music stuttering, audio not syncing and then breaking with cut scenes. Then game breaking levels of stutter.
I mentioned that I never thought his new system was good (his 60GB was fine, he just wanted a warranty, urgh).
So we tried my copy in case it was the disc, no luck.
I suggested it might be the hard disk combined with the more budget internals of the slim.
So we first backed up and deactivated the system. Then removed the 250GB HDD, reinstalled the 160GB (patching from the 3.73 firmware on Playstation.com). We tested video whilst downloading, no problems. We the tried Uncharted 3 it had the odd hickup, but was now an unbroken game. We then restored from his backup, reactivated the system. Tried the Video test and Uncharted 3 and it worked fine with only the very occasional stutter.
I have to my knowledge noticed no stuttering at all on my 40GB.
I am guessing that either the 250GB drive he had was badly set up or clashed with the cheaper components of the PS3 Slim.
I hope this helps anyone with their Uncharted 3 stuttering. I can guarantee you I won't be 'upgrading' to a PS3 Slim any time soon. Although this is purely anecdotal evidence.