Ahhhh Mr Beery i have found the problem
I think. And forgive me if your mention this many times. When i load the stock game of SH3 i have my firewall on, Antivirus running and Spybot loaded, cos i sometimes head to the multiplayer. (i have my firewall to allow SH3 to run etc.,) Having these on never effected my gameplay in single and multi. But it seems it effects any mods i throw on. Well i turned off all of the above mentioned, started up commander load my career and she runs! no errors!
Fixed.
I like how your got the updated commander personal file very nice.