is your wiimote fully synced to the wii using the red buttons or did you just hit a button when you got the wii and it just worked?
this seems to be happening a lot when ppl dont fully synce the wiimotes and when homebrew reload IOSes the wiimote donst resync
example
i synced my white wiimote to my cousins black wii and hacked it for her, went to load wiiflow on my white wii, it loaded thru a forwarder,remote desynced once it loaded, tried to connect the wiimote and nothing happened just constant flashing, i had to reset the wii fully resync my remote to my wii and all is well
but this might not be the case for you as you MIGHT of FULLY synced the wiimote