Are you using the same serial cable with the Mk1 as you were using with the Mk2? In both cases, are the players plugged directly into the cable (good), or are you using the docking sled (bad)?

If so, I would say that a harware problem is a possibility and should be investigated. If that's true, then no amount of "fiddling" will fix the problem short of repairing the serial port fault. Upgrades require the serial port, period, and if that's faulty then there's nothing else you can do.

Are you sure it's not just a frayed cable displaying intermittent problems? For instance, maybe the mk1 and the mk2 are on different parts of your desk, and stretching the cable the extra 12 inches to reach the Mk1 is causing the cable to lose data?