I noticed the same thing. Top says Audacious is chewing up ~50% of the CPU and pulseaudio is eating another ~30%. Between the two my CPU is pegged, so I'm guessing any additional load (like pre-filtering the audio through the EQ) causes the audio to skip.

I see the same skipping effect by starting a couple of other desktop apps (Gkrellm, vncviewer).

By comparison, CPU usage for lxmusic is in the 15% range with PulseAudio still eating roughly 30%. The native N900 media player uses <10% and pulseaudio doesn't spike at all.

Using that much CPU to play music in the background leaves little room for running other apps, which defeats the whole purpose of running a full desktop on the N900...

I'm going to download sources for pulseaudio and profile what's going on (money says there's a busy wait in there).