I had that message bug me for a few days, but I got the message at the end of a patrol when I tried to get to the SH3 Commander's patrol report.
I got that message each time with two different kaleun. After much thread searching to no avail

, I backtracked and realized I had promoted each of the characters manually by going into the career.cfg in the SH3 Commander folder and changing the rank= figure. Turned out that SH3 Commander did not like that as there obviously was a date mismatch somewhere. Once I changed the rank= code back, no more error message!
Sorry to ramble. Did you by chance change something manually like I did?