Generally it's a mix up between 8 & 16k versions of the skycolor Env files or the Scene.dat file, I'm not familiar with some of those mods, just check them out one by one till you find the one causing the problem.
What I would do is roll back SH3 Commander then run SH3 only, select the Navigation academy & check it out, if problem is there then quit the mission, Alt-Tab run JSGME & disable a few mods, then go back in to SH3 and run mission again, keep going till the fault is gone, will then be easy to narrow it down.
If all disabled except the GWX 16k mod and still not fixed then it will be a corrupt install, hope this helps.
