I think it was only a couple launches for me, and I didn't go nuts pirating. For all I know, you could probably just launch and dock right away.
I'll take a guess that maybe a script got messed up. Here's what I would try: duplicate the last couple missions you performed. For instance, if you had to go to xyz system and do abc, then go back to that system. I usually dock at whatever station happens to be there, just to be certain I didn't miss a script trigger. Then go to the next step, and so on until you've basically re-done that mission. It may be that you simply didn't complete the last step, which is usually going back to talk to whomever gave you the mission.
Also, take a look at your Objectives on the HUD; Shift + O opens the Objectives You might find that this previous mission still has something left for you to complete. If that doesn't help, let me know and I'll try to revert to an old save and maybe see what's going on. I had a couple weird script issues this playthrough, though I don't know if it was because I took some time exploring and accidentally triggered something I shouldn't have. And I think I screwed something else up somewhere since I don't have the Kong as a trading partner (just started Act 3) though I could have sworn I've traded with them on previous plays.
Oh, just thought of another. There is one mission, I think in Act 1, where if you don't deal with it right away it will be taken off your objective list. I think it was one of those group meetings with the Stepsons, and I decided I didn't want to deal with it right away. I launched, farted around for a while, came back to the base, launched again, and found the waypoint was missing and the objectives were no longer listed. Fearing a messed-up script I reloaded an old save and didn't notice any problem after that, beyond not trading with the Kong.