To reproduce:

1) Start the remote buddy setup wizard and bluetooth "add new device" dialog, leave these running. 
2) Create a Wii device in the harmony app, and initiate pairing: neither OSX nor RB detect the device. 
3) Delete the Wii and add PS3, then attempt to initiate pairing: if you're lucky, the hub will flash as a Nintendo Wiimote, then switch to BD remote. 
4) For some reason, RB will recognize the Wiimote but not the BD remote. It'll attempt to pair. 
5) Pairing should be successful, and the Hub is added as a Wiimote 
6) Remove the PS3 using MyHarmony.com or the app, and add a Nintendo Wii. 
7) Sending Wii commands should now work.

I hope that we'll get a more elegant solution in the future.