I am having the same problem. I was under the impression that it was due to the fact that I'm running the server software and the terminal all on the same computer (only a piii 450, LoL).

None of my NPC's would follow waypoints with a full spawn2 database. However, due to my storyline, I am having to ace everything (including factions) and starting from scratch. I now have no problems with waypoint programming and am currently testing my capacity for each zone I've included.