Hi. Keyboard encoders.
I was trying to get around the whole windows changing my controller ID thing with MAME. I had all 3 joysticks plugged into a usb hub before. Then I tried plugging in each stick into it's own usb port. That's when the weird issues arose. I've since gone back to the hub and I've secured all my connections in my arcade stick box better, and so far, things are working properly. It's possible that when I move the arcade stick box around, there were lose connections and windows would change the ID's.
I know there's a fairly complicated method with MAME for setting permanent ID's, but I'm trying setting the .cfg files to Read ONLY for now and seeing if that holds.