Something to consider: Are you using the map functions? I know that I can get small freezes if I've got npc's enabled on the maps and there's a lot of npc's/pc's (if I turn on PC's in PoK, Baz, etc, I'll lock up for a second). My assumption was always that this delay is caused by MQ changing the map file to show spawns.
I'm not sure if MQ will still write to the map file if the map window is closed... but it may. Something to look at.

