There's always the possibility that there's some other cause, but like I said, if Wii remotes are working I really don't see why the pro controllers wouldn't. The pairing is exactly the same.It is very odd. My "authentic" pro controller really looks like the real deal. It has alle the symbols/marks that copys usually dont have. But I bougth the wii u system second hand so I really cant be sure that the pro controller indeed is original but it would surprise me if this was a clone.
Could it be something else ?
I have noticed a few occasions since 13.0.0 where my Wii controllers didn't pair until after a reboot, so you could try this if you haven't already. Not sure if reliability decreased since the update, or whether it's just some instability I introduced during development/debugging.
Probably not the cause, but could also be worth checking your bluetooth pairing database is not full. You can do so with my btdb tool. I'm not actually sure what the expected behaviour is once you exceed 10 paired devices. I would assume it just overwrites the oldest one and carries on, but I know at least internally that hitting this limit generates some kind of error status.
If all else fails you could try making a log of your pairing attempts with this debug build of 0.6.0 and post it here. The log will be created on your SD card at sdmc:/bluetooth-mitm.log