If you're using the software equalizer, basically Rockbox on iPod is currently not fast enough to decode audio and use the software equalizer. There's work going on to fix that, but I'm not sure when we'll see results from that.
For the moment you can try either fewer bands on the software equalizer. I have heard of some success with using one or two bands.
Your other option is to use the hardware equalizer, but be aware that while the user interface lets you set five bands, only the first and the last band actually work.