I've been having the same issue.. have also been having it with BFBC2.
Things I've tried so far.
Updated drivers
Uninstalled Physicx
Changed resolutions
Tried fullscreen and windowed
But still every time I start up I can play for about a minute maybe two before it will graphics crash and need a hard reset. This happens in menu or in-game.
Some people think it's because the game isn't running/detecting the right Directx version.. as that was there fix for BFBC2 but I have yet to confirm that.. will do so momentarily.
EDIT: Okay yes that issue fixed my crashing for BFBC2 but they don't seem to have a directx version setting in the ini files for Alpha Protocol.. so hopefully Obsidian will fix this or some other fix comes out asap.