A couple of thoughts:
Did you start a new career? If so, did you make sure the year and flotilla you selected in Commander were the same as what you selected in the game interface?
If not, did you mod the game while you were still mid-mission?
Did you test the unmodded, patched game before you installed the mod? [I just reread your post, and it sounds like you did.]
If that's not it:
I would try rolling back SH3 Commander. Then use the program removal tool to actually remove Commander. (I'm not sure why this works, but it has helped me before.)
Then, the best thing to do is start over from an unmodded data file patched to v1.4
Reinstall the mod, then reinstall Commander on your computer.
Of course, if you saved your data file after you patched it, you can just delete the SH3 data file, replace it with the saved one, and then install the mod, and then commander, in that order.
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