just upgraded my old fat 40gb ps3 with a 160gb samsung HDD, when i turned it on the message came up indicating that the system software cannot be run correcty, so all i did was put in a brand new game that has a firmware update (modern warfare 2) and it worked. although you would have to go through the whole process of setting up your console just like the first time you turned it on, then i just restored my backup game files like usual. i think the problem lies with the old ps3’s where the system software is actually on the HDD rather than on the console itself.

hope that helps.