I am having same issue with my PS3, I think my HDD has some bad sectors, I can play most disc based games, some of them work fine like MGS4, Dead Space and Assassin's Creed. But GT5, I got shutdown error with red light blinking when loading certain tracks or location in main menu, Uncharted Drake's Fortune, I can play bonus videos, cutscenes, but when I load certain levels or play from beginning, it will shutdown right after I take control of Nathan.
Tried full format, low level format, scan the HDD with PC utility, it says no bad sector, put it back to PS3, clean install 4.31, insert Uncharted game, shutdown every time I took control of Nathan on first level.
The issue also happens on PSN games on the HDD, some of them causing shutdowns, even scrolling the game list will cause it to shutdown or streaming movies from my PC ( randomly )
Tried to install Windows XP on the HDD, I got CRC checksum mismatched blue screen error for NTkernel32.dll when running setup process after copying setup files + restart, I guess my HDD have serious issue.
I have no heat issue, running PS3 slim 2009 with top cover off, replaced thermal paste after 1 year of owning, the fan never goes above boot up speed, really cool air ( just like when booting up ) from the fan even after 24+hours running. The fan also never increasing it's speed when running heavy games like Uncharted, MGS4, GTA IV, GT5, Fallout 3.
Strangely Fallout 3 GOTY is not affected, I played for 8 hours straight couple of days ago, no shutdown or fan ever gone faster than idle speed.