I'm not completely sure, but as fas as i remember, only the one that depends on chosen class. Other skills you can up only to Expert level.
Kornel mentioned about "unlocking master level", so I was not sure what to think about it (and I am still unsure :P ).
As for now, it works like you mentioned - tested on one (already dead from boredom) Elite Marine :) .
I noticed one small silly bug though - after taking a master level in skill, there is another level - "maximized".
You can't take it, but there is still the cost (in experience points) next to it.
In my opinion it would be better just to show "master" with a special color (golden/yellow or sth like it) and without a cost to a "next imaginary level".