Spoke to WO last Firday regarding the flaky desk issue. He suggested that I consider the COM port being poorly supported by the OS. He says that modern machines do not support COM very well and it's possible that we won't resolve the problem with the current OS/hardware. I did a bit of research and discovered that the possibility is certainly there, but as I have no really specific info about the way the COM port talks to the OS in this case I have no simple way of diagnosing the problem.
Wayne's recommendation is to rebuild the older box and see if it has the same problem. I'll get right on that.