I have the same problem right now, the only thing that fill my tanks up is raw oil, not fuel, not lava I haven't try with water.
A couple of things that I find out on my tests:
If you fill the tank with a fuel bucket the tank fills up like it should.
The fuel don't even show in the refinery mini tank, only the oil.
I thought the problem was the texture pack or my video config, but thanks to the first point doesn't seen to be the case.
The problem is not in the refinery because the lava has it as well and it doesn't need a refinery, in the pipes maybe?