Mike
I had this problem a few weeks ago; assuming you are using SH3Cmdr.
Has the month changed during the patrol, as I think that what triggered the situation for me.
To get round this open up the relevant career folder and go to the careers config file. Open it with notepad. Scroll down the details of the last mission and there are two lines that read something like career end and war end. Both of those will now say true, edit them to false and save. open up SH3Cmdr again and you should get your career back.
May I suggest you change the realistic career option for it (if not I suspect you will get a repetition).
Hope it helps.
Just read the added comment. No mods? that being the case disregard the above. :rotfl: