Anyway after fiddling around on my xp netbook I got it working... sort of. It seems that the motherboard firmware I uploaded, when asked for the the extruder temperature (M105), reported the extruder temp AND the heated bed temp. Well the Reprap software didn't like that, not one bit. There were NullPointerExceptions and IntegerExceptions everywhere as it clearly tried to parse "0 B:0" as an int. Luckily being open source, and having the source at hand, I removed the offending code from the firmware, reuploaded and - tada all was well. I was going to test more of the electronics but, that requires making up some cables to the right length, so that will be a job for monday.
The usb/serial adapter and motherboard with the happy yellow light of workingness.
Look it works, g-code commands being sent and replies being received, hurrah!