No I'm using EB.exe, but I did try to run under Ferromancer's BI mod and when I couldn't get it to load I deleted and use EB.exe, but maybe it left the "bug" behind.
Thanks for the help though guys, I actually think it's a bit more realistic this way I have to think about keeping Generals in supply, it's just a little annoying with level IV govts when I get the inteloper trait in settlements.