This has happened to me many times in the past, the problem starts once the core is loaded though, RGUI's colors stay the same for some reason but scroll through the options and you'll notice that it is indeed slower. The core that usually got this problem was fceumm like the op states despite all the cores using the same method of loading.
Simple fix would be to load the .dol through WiiXplorer or something similar. I've been using the more recent unofficial builds and haven't encountered the problem so I can't say for sure if it's fixed now but it looks like it. So yeah I think the problem starts the moment you select the core to load and not in any random area.
Crop overscan shouldn't be the cause, I've had this problem in 0.9.9, before that feature was implemented.
That's a good shot of the problem if you'd like you should post this in the libretro forums, but there is a chance the problem is gone in the latest source.