I don't see how a software upgrade could have caused a drive failure.
Something you might want to try is formatting that "bad" drive from scratch and seeing it if still exhibits problems.
This makes me think though...
At the moment, the player/emplode software isn't terribly helpful in telling you if there's a problem with the disk drive. Instead, you just get mysterious errors and behavior problems that are hard to track down. I wonder if there's a way for the player to notify you on-screen if it gets certain drive errors.