I just wanted to mention, I had the same problem with my friend's Wii, with the Wiimote not being recognized at the Scam screen.
He lives about 3 hours away in the boonies and has no internet access, I had installed CIOSCORP at one point several months ago so he could his kids could wreck backups discs instead of their originals. Last weekend when I went to upgrade his system with USB Loader, BootMii, etc, my first plan was to install BootMii and make a NAND backup before proceeding. Of course I wasn't able to do this right away because the Wiimote wouldn't be recognized at the Scam screen.
To make a long story short, I used the Offline 4.0 upgrade method (from
this guide), after upgrading I tried installing BootMii and it worked perfectly.
I know others have already posted the cIOS36 as the reason of the problems, I just wanted to mention I had also run into it and resolved it just by upgrading the system to 4.0 manually (overwriting IOS36 in the process).
My friend now has the most souped up Wii for about a 100 mile radius, lol!