As far as not getting credit for the FE, here's the tip I've learned through 2 years of buggy programming: Once you think you've completed the mission, DON'T LEAVE THE SYSTEM! OPS will try and get you to warp out, but don't do it. if the mission box in the right now says 'report to starfleet' or whatever, go into your missions, find the green checkbox, and turn it in. THEN you can leave the system with your credit. In theory, if there was any customer support, that would be a good place to call in a GM and show them you were finsihed and not getting credit, but we know that takes days, not instant help as advertised.
I used to not get credit on occasion, opened tickets, and eventually they agreed I had completed them, but that they didn't have the power to award me the mission completion anyway, so maybe I should try dropping the mission and starting over. Thanks for the help, guys!
Reason I didn't try this at first on the FE is that I thought there might be more when you get dropped in Bajor. Not sure why the mission completes in the DS9 system and it still makes you go to Bajor, though. Functionality-wise, doesn't make sense, as the mission is complete before that. Eithe warp out to sector space, or give me something to do in Bajor. Along those lines, IN-Universe, why would Bajor be a safe rally point? Shouldn't they get out of the solar system? 2800 enemy ships in the system, and their big rally point is about 5 minutes away at low impulse?