I use that registry remapping thing all the time in windows, and never have a problem. I'm betting on the adapter being the issue, as I do this all the time, with many different keyboards, with no problems whatsoever.
Just to ask: are you doing it by hand, or are you using something like keytweak to generate the mapping? Basically, what registry key are modifying, if you are doing it by hand?
In fact, that's part of what attracted me to the HHKB, honestly.