I think that they should at least release the digital version, not as costly as printing a crap load of discs that they think they wont be able to sell. Then when they are ready to release it on all systems they can just release it with a patch if there is any new content they want to include...
Mine has done the exact same thing. Only thing I noticed was it happens when I enabled codes for new super mario with ocarina. After doing that one wiimote causes system files corrupted warning. Other than that no problems. I just reset it and use the good wiimote.
I was wondering about something similar. I have a passkey1 and I recently got a DSLite. Is it possible to send Flashme to the DSlite through the wii which would save me a little cash so I wouldn't have to buy the newest Passkey and I can continue to enjoy my DS homebrew on a brighter screen...