Bug in the Zero-Altitude setting
 

If you are building a custom map over hilly terrain, the zero-altitude setting no long functions for spawning NPC groups. The zero-altitude setting should override all terrain features; however, the only way to set a NPC group over a hilly section of the map is to use the Terrain setting and play around with the Y coordinate until you get the NPC group to be where you want them.

Armand Falconer, Sector 31 ANTKB
Published Missions: 3 - Rescue the USS Odelia, Winters Blade, Winters Chill

Probably should post exactly what map you're using along with the mission title and short code.