I had this problem where I downgraded to cIOS rev10 from rev14 that made apps such as neogamma load up to a black screen. It made WAD manager disconnect my Wiimote (without being able to reconnect) when selecting IOS249 and when going back into any cIOS install the same thing would happen to the Wiimote.

I search through many other threads noticing there were a few people with the same problem, but they were not given a straight forward solution.

It is very simple though... and I'm not sure why it took me so long to think of it.

Use AnyTitleDeleter and delete IOS249 completely, then go back into Rev14(or whatever version you want) Installer or WAD manager and re-install cIOS.

Hope this helped anyone with a similar issue.