I can't skill-up my Lt.Cmdr skills even though I'm a Lt.Cmdr level 11 why not? I can add skill points to my ensign skills but not Lt.cmdr, any ideas?

Do you have enough skill points? Lt.Cmdr. skills are much more expensive, (roughly double) of what Lt skills are?

And you did complete the promotion mission to Lt.Cmdr. from Admiral Quinn???

I have 17k skill points and I am pretty sure I completed the mission from Admiral Quinn that was automatically assigned to me when I reached level 10 and got a free ship, Nova class btw .

But the skills under the Lt.Cmdr category are not activated. The arrows to assign the skill points are not there. What am I doing wrong?

I just noticed that after the patch, the skill levels don't follow on, the level you need for say captain is more than the number of points you need to complete commander. So you actualy need more points in commander than it says to unlock the ability to level up your captain skills. This is true of all levels.

Also you need a certain amount of points spent in the previous rank before you can add anything to the next rank in case you didn't know that.