Upgrades have a lot to do with chaging what's stored in the flash memory of the player, so you won't be able to upgrade by pulling the hard drive out...

The most obvious problem would be if your baud rates were mismatched between the player and the computers you were using. Perhaps someone messed with your Mark 1 and set it to something funky? Bad cables are also an option, but RS232(serial) is a very forgiving protocol, you wouldn't beleive what i've seen it run over... Can you post a boot log so we can see what the dropped characters look like?

Matthew