Yeah, I have a career with this problem, the one I'm on now in fact. I just edit the patrols_0.cfg file in my captain's career folder before every new mission, and manually put in my next patrol area in the last patrol section in that file. It's the second career on which this has happened to me, and I've found no cure. It happens at the start of every mission now.
Oddly though, I'm getting missions assigned in months where there are no missions supposed to be offered by what I see in the Flotilla.cfg file, (first half of 1940 in 7th flotilla has no mission areas listed for January to like August), so I've assumed that after August 1940, it might start giving me patrols again. Only time will tell. I hope I don't die before then.