The mission is the one at the end of the second campaing, right? I had no problems destroying the Fazrah base and getting the mission. The mission was to destroy the Fazrah base in Knoglam system and report back at the Abbidon Listening post at Karnak IV. For me it worked fine. After I destroyed the base I got 36000 credits and was informed to return to Karnak IV.
Are you sure you destroyed the right base at the right system? For what I can tell there is only one base in Knoglam.
oh. Well I think I know why you can't get the mission. If you leave the system and then return you can't complete the mission anymore for some reason. I don't know why. I have the same problem with the Jinook Sithrak starbase. I went to the neighbour system to buy toxic injectors and then when I returned and destroyed the station I didn't get the quest. Oh well, I guess I just have to go through cheat codes.