Rebuilding Nav Mesh During Play- AI not moving?

So I am working on creating a procedural top-down dungeon crawler. I have it set up so the rooms branch out forward like a pyramid. Every time the player gets to a door, the next room loads. I have one giant nav mesh and I use a console command to rebuild the nav mesh every time a new room is loaded. Because the rooms are relatively small, the impact to performance is minimal. However, the AI moves on my test map, but not on the procedural map. I would imagine it has to do with rebuilding the nav mesh. If anyone knows how to get my AI moving I would really appreciate it.