Did you ground all four switches on the and the buttons? I can't remember which color wire is the grounding wire for the buttons, but I opened up my handle to see the ground wire and it was obvious.
I have a set up similar to yours, connected to an Ultimate I/O board. For initial testing, I would open up notepad and move the stick and press buttons, and see if the chars came out correct in notepad.
My FE (Mala) wouldn't see the mini. But it works just fine in MAME.