Sounds very similar to the issue I have with my 1800 pcb. Keys register in JigOn but nowhere else.
Did you get anywhere with yours?
Leeku has been very helpful going back and forth through multiple PM's suggesting things to try to fix it but I still haven't figured the problem out.
I tried the board on another PC to verify it wasn't the computer or driver issues. I also messed around with the firmware some more with no luck.
All I can get is still key presses in jigon and even got it to do this (see the input in the file name box)
Show Image
(http://uploads.tapatalk-cdn.com/20160510/f88c9862a7ffbe00b02e5e44f5a567ab.jpg)
I'd prefer not to have to ship the PCB back to him to get it fixed so my next step is to reexamine all diodes and possibly swap out the switches. But it all worked fine to begin with so I'm not sure that will gain me anything.
The LED's for num lock, caps lock and scroll lock respond to other keyboards connected to the computer but not to the keyboard itself.
This has been the strangest issue I've ever had with a keyboard.
I'm not sure if this is basic troubleshooting or not but those outputs mean that the keyboard is still in "bootmapper" mode. In Jigon, if you go to Keyboard>Disconnect it should put it back into regular keyboard mode. Also note the default layer it's on, my TX1800 with Leeku 1800 likes to reset its default layer for no apparent reason all the time.