I was going back to finish the "Slowing the Prejor Advance" mission. Before I had already complete 1 iteneration of this mission and already had the Exotic Pulser equipped on my ship, and the mission when it was reposted said I had finished this mission 1 time. But after finishing it the 2nd time, I got no pulser and it still said I had finished it 1 time. So it looks like if you had done part of the missions, even though it shows you've done them, its making you start from scratch.