Debug console? Windows debug console? Teensy debug console? Keymapper debug console?
I've just read the help pages for the 9/2 beta, and I think I know what's going on but don't have a programmable keyboard here to test it.
in 'Qaz software, you can map a key to the console. Then, you build and flash the keyboard with the has-a-console firmware, then fire up notepad or the like and pretend you're at a teletype. Press the debug key, and it will type out a menu, and you can use notepad to enter commands, such as toggle basic mode (help file does say its called that). Save the config changes (maybe?) and reboot the PC -- try using it then.
I get a similar problem though, with my ergodox. During boot, it goes to a grub menu, and the ergodox arrow keys are useless. But if I warm boot, sometimes it will work. If I have a regular USB keyboard attached when I warm boot (never first the first, cold boot) then the arrow keys on the ergodox (mass drop / benblazek code) works fine.
I just sold my phantom but I've warned the user to follow this and a few other threads so maybe he's reprogrammed his by now...I'll ask about it, actually.