Did you go speak to Admiral Quinn first? I know one time I went into his office and it made all kinds of sounds like I'd been promoted, but it didn't reward me so I had to leave and come back.

I know you said you spent all the points you need, but just to be sure, I find that the step from Commander to Captain usually requires you to spend a couple hundred more over cap. I think it has something to do with the cost of the tiers and the way they were divided out. You can hit Commander 11 but you still need to spend a few hundred more points.

As for getting help, you can click the "?" to the right of your mini map to Request GM Help or Report a Bug (help can take a long while, but it's an important step). The other option is to follow the Support link at the top of the forums, go to the Atari sight, and file a ticket through there. I've had better luck at getting responses when I use the support site.

http://www.atari.com/support/startrekonline

Good luck.