I refuel up to 20,000lbs with no issue, without fuel tanks the most you should be able to take is 16,400lbs however there is a bug at the moment where if you jettison your tanks it will still fill you up to 20,000lbs.
The 11,900lbs thing is something I've not seen yet. Even with the probe switch in FUS Ext you should be able to get 16,400lbs.
I'll take a look at the instant action mission and test it out to see if I can reproduce.
@Rikkles, check out this tutorial video I did, hopefully it will help you out.