An update: I've been unable to do any further experimentation until today. Here's what we tried, and the results:

1) Uninstalled the program, cleaned registry to remove any stray entries that may have been orphaned.

2) Re-installed AFPD to drive E, adhering to the recommendations for Windows Vista, that AFPD not be installed to the default path on drive C.

3) Installed the patch file that you specified earlier in the thread.

Result?

The rudder is on the right stick where the ailerons should be, and the ailerons are on the left stick, where the rudder should be. Elevator & throttle are ok.

I don't understand why it's not coming up in Mode 2. Please advise.