When SH3 Commander is used it applies/makes changes to SH3 Files. Therefore it is nessecary to always roll back SH3Cmdr before you add any other mods/files which could change the same files.
In your case I have assumed that you enabled the 16KM ATM mod without rollingback SH3 Cmdr.
My suggestion would be to rollback SH3Cmdr & disable all Mods. Then start SH3, via the SH3 Shortcut, and see if you still have problems. Start with a new campaign, do not try to use any saved games. If it works then enable your mods and start via SH3Cmdr.
Good luck
EDIT - SH3 Cmdr roll back does not roll back SH3 it just removes the changes that SH3Cmdr made.
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