Using 1.07rc5 I just managed to force the automatic surrender of a fort/army - message said I took 52000 prisoners but when you check the F9 page these prisoners are not recorded. Perhaps the problem is because the prisoners are not taken during a battle ?
Another problem I have noticed is that union generals who are commanded to form divisions seem to lose some of their strategic-offensive-defensive points bonus - the reductions seems almost random. This only started happening from around mid 1862 onwards to the union side on the april 61 campaign scenario.
I have a save of my last turn with the pow problem if it is required - just let me know.
btw this is an excellent game - well done to the ageod team.