All nintendont stuff like games, dol, controller and ipl are in the SD,
I can move everything to a usb device and leave the dol in SD. I'll try
It almost sounds like it's ignoring the controller ini. Did you try turning on OSReport and see if it mentions anything in the log? I'm not sure if the ini loading is logged but it wouldn't hurt to try.
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Hmm... I'm looking at main.c and it looks like the HID initialization is commented out? Did it get moved?