My stuff is all on Win10 & have had no problems software-wise.
That does sound odd. These things are usually pretty simple to troubleshoot & fix. I can't think of anything else simple to check & it sounds like you're pretty confident in what you're doing there so it sounds like it should be working...
Is it just those 1 or 2 keys that do that? Everything else works like it should right?
I'd check over at Build Your Own Arcade Cabinet http://forum.arcadecontrols.com/ & see if you can find something in there.
If not, definitely shoot Andy an email. He should take care of you no problem. (That is, if that's where you got it from)
I'm sure someone else around here has some other ideas if you can wait a day or so...
Pessimist: Oh, this can't get any worse!
Optimist: Yes, it can!