I got it with the controller parts already soldered so it already had the firmware when I got it. I tried to reupload the firmware to hopefully reset everything including the key mapping to see if that would fix it. I did upload the firmware you said (ps2avrGB_NKRO.hex) and it seemed to fix it. So then I went back to the key mapper and uploaded the default mapping file and that also seemed to work. But then I went to change some of the keys so that I could control the LEDs and it went back to the non-working state like it was before where it acted like a few keys were stuck down. Also if it matters, the first time I did the mapping after I soldered the switches and before I soldered the LEDs, I didn’t use the default mapping, I just individually mapped every key and that worked just fine afterwards.
