I have this same problem. I logged out and back in, changed maps, closed and opened inventory... I still don't have the 50K Dil Ore or the 250 Marks Of Choice. I don't *think* I got the 500 Fleet Marks but it's hard to tell because I don't remember how many I had before I got the rewards.
I could have sworn it wasn't there this morning, but I had the box with the Dil + Fleet Marks + Choice Of Marks in my inventory when I logged in just now. All solved, thanks.
Answers