Mark Emplode does the same thing, so perhaps it's the protocol. One thing I've noticed is that if the buffer is full, or rather if there is enough music queued up where it should be full, an append is less likely to happen. But if I only have one song playing in a playlist, any additions or insertions cause the pause. Does this make any sense? I think it was worse with 1.03, so the empeg guys might know the cause of it. I remember it being a bug fix.

EDIT: Other times I've been hit with this pause when there is a lot of music in the queue, so maybe it's a matter or timing or coincidence? I don't have the knowhow to really know what's going on. My "buffer" theory doesn't explain why the web interface wouldn't have this behavior.