not sure how much this will help, but compaq back in the day, did this one "clever" thing where they would partition an 8meg section on the hard drive to store the bios. so when my friend tried to upgrade the hd for his mom, the comp wouldn't work. he spent the whole weekend trying to figure out wth was wrong w/ the thing, until he stumbled upon a solution. (this was a compaq desktop back in 1999, so it may not apply in your situation..)
i hate how everyone company tries to do their perprietary get up w/ their machines..