My bad - didn't even see your last post there - posting half asleep (or more).
Probably a stupid question but....did you try hitting tab, and going into event remapping to config up, down, etc.
If so, did it detect anything when moving any controller hooked up to the stelladaptor when doing the remapping?
IIRC, stella detects up to 2 stelladaptors (ignores any more). If it is actually detecting any usb HID's, anything after
the first two would be ignored. You may have to unplug or disable other usb devices for it to detect the Stelladaptor.
Sounds like a bit of fun with trial and error.