I'm not exactly an expert, but GWX 3.0 comes with mods to be loaded in a certain order. Also, if you use SH3 Commander there are options that must be unlocked. Recommendations:
1. - Prepares a clean installation.
2. - Read the Manual, to install properly the mods that came with GWX 3.0.
3. - Search which options of SH3 Commander are compatible with GWX 3.0.(I do not remember right now).
By the way up your list of mods, maybe there is a conflict with any of them.
Regards.