@disorder This could be caused by how configgen "detects" pads. Can you make a pastebni of ~/.emulationstation/es_log.txt ?
Maybe this helps?
I just tested it on my Pi2 and there was no noticeable lag, at least no more that I remember the game originally had XD. Maybe you TV needs the game mode enabled? That is often a source for lag.
Worked well, thank you.
@disorder While I cannot help you with a solution, I can verify the problem (or at least a very similar one):
As can be read here, changes to the "Input" menu in retroarch are not changed, at least some of them (player input type). Sadly noone could help me with a solution yet.
Greetings from Germany
yeah, that does happen to almost everyone. Just press the dpad and tadaaaa. In fact i almost like that behaviour ! That way i know the pad has paired