v1.0.142.0 released. The problem with v1.0.136.0 was I thought that the materials were laid out sequentially in the file (along with their map references). Turns out to not be the case. Thus I had to add a flag to the map reference class. This flag denotes whether it's map reference was found or not. After the app loads all the materials it goes back and verifies those with maps have all their map references defined. If not, it searches for them to define them. Saw this problem using the bunker.GR2.
Now I'll look into this bunker problem Privateer spoke about