well that's two days worth of badges that were going to go toward my disruptor setup down the drain, did one FvK and one FvF lost the FvK, no credit, won the FvF, no credit. To annoyed to try any more.
I had never had this issue until after the 1.1 patch and the pvp daily mission got shifted over to Icheb. Yesterday it took me 9 salvage ops to finally get the daily to complete. I could not find any real rhyme or reason to when it worked and when it didn't. Winning doesn't cause it to work. Hell, I even tried throwing a match for the sake of curiousity and that of course also did not work. What team it assigns you to also seems unrelated to it. FvF, FvK, there were instances of both the small and large varieties working and not working. I can find nothing that seems to be a cause of this issue. It's like it just...happens.
Was happening to me as well last night. Played 5 capture and hold and only finally got credit for my 3. Game was causing a black screen crash after most of those missions when arriving back in sector space as well.