Classic Controller Losing Connection

A few months ago or so I purchased a black classic controller pro for use with homebrew applications and other games. The controller works fine with normal Wii games, but if I use it with any homebrew application, it randomly seems to lose connection with the Wiimote. If I replug it, it seems to work, but sometimes I have to reset the application entirely.

Recently I got a normal Classic Controller, thinking that the black controller was at fault. However the same thing happens, although it seems to take longer with this controller. So the hardware is not at fault at all, I tried plugging it into a different Wiimote, replacing batteries, resynching the Wiimotes. It happens with all homebrew applications, and I can't seem to find anyone else with this problem.

I really don't know what to do, I have no idea where the problem is lying. If anyone could help or at least suggest an idea, I'd really welcome it.

This might look that it has nothing to do, but it does to some extent...

What System Menu version are you running on your Wii?
What Homebrew Channel version are you using?
Do you have any cIOS/patched IOS installed? (If you don't know what these are, drop this question)

My system menu is 4.2e, and my homebrew version is 1.06. I realize that's a bit outdated, but it's long after the point when classic controllers was made compatible.

From what I can recall, iOS36, iOS60 and iOS70 are patched.