This game is very buggy Brad, hence why there were so many ships that you couldn't beat. It scaled the difficulty up because you entered the system with 4 party members. Even if they aren't present, it will scale it up. So next time if you're done with a party leave the group.
I found this out the hard way when we had a social party going on with a few GB members, and all of us were getting raped on our personal quests. We ended up sticking to Fleet chat because the game is just too Beta-y. :-(
