Hi There UlyssesSGreezie try installing SH3 outside Programe files x86
I had same problem on windows 10
Start again delete your install and also delete your SH3 Folder in Your Documents
Make a folder in C:/ Called eg Wolfs of war or anything you like then install SH3 into that folder
and install the Commander Mod into that folder also
then run your Stock install of SH3 it will make a SH3 folder in your documents
for your career saves
then place all the GWX Bin Files including the Commander mod Gwx Config Fiile if your using it into the SH3 Folder and run the GWX3 exe if all goes well no error messages then install Commander mod into the Wolfs of war Folder then launch the Commander Mod File it will ask you where your SH3 install is located all went well for me no issues or error messages then I launched the GWX Commander MOD Config File that I put in the SH3 Folder and all is fine Hope this helps feel free to reply if you need further help
Inside Wolfs of War Folder