Check and make sure the Map you're choosing allows the NPC to be in the Middle. If it doesn't check what map might allow that.
You can do this by selecting a map and reading the info that it gives in the MA creator on the right near the map description/visual.
http://tiny.cc/ArcaneDefenseItems
This is a bug, nothing more. Please put away the tin-foil hats, there's nothing sinister going on here.-Protea
http://tiny.cc/WhatBeatsADragon
As near as I can tell, some of the tech maps, due to the funky elevator linking in them, don't have a logical "front" "middle" and "back"
If you look at the layers on the MA, there are spots where layer four would actually be considered the second floor when you're playing through the mission. Its my best guess that this is what fouls up the spawn placements on these maps.
The problem is that Middle tends to cover the areas that Front and Back don't. In many Tech Maps the hallways leading up to the first big room (which is the Front) are considered to be Middle. I found this out when experimenting with boss and battle placements and seeing where they appeared every time I changed the location settings.
One bug that I can't squash in my mission with medium length Tech Maps: I have the escort NPC location set to "middle", but every tech map I've tested sometimes puts the NPC in the very front, before spawns set to "front". It's not consistent, so I can't just swap the spawn location in the mission settings. If anyone knows of a tech map that [u]always[u] spawns NPCs and items correctly for front, middle, and back, please let me know.