Obviously, I have not seen you game, but I did have something similar happen to me and, I hope this might help.

If it is the same, when you select a mission you get a  message stating that you must accept the loot before being able to continue.
On that main screen, I think it is the system map, in the top left corner is a small red button; if not you certainly click there about.
That should 'accept' the loot that is being held for you.

As I said, it may not be the same set of circumstances, but I hope it helps.

Cheers. :)