That is odd, it's almost always the other way around. If the seals and sealing surfaces are good, it has to be a plugged vent on one of the two.
The transfer case tube may be clear, but it could be plugged inside the case. I check those by removing the fill plug and putting a light shot of compressed air through the far end of the tube. It can get a bit messy, maybe put a drain pan down.
Other than that, the transmission may be to blame. That's a manual transmission, no vacuum modulator or vacuum switches or anything right? Every transmission has a vent, I think it's one of those little flapper valves on a T5. It may be releasing pressure when heated up, but not let air back in when cooling down, leading to a vacuum in the gearbox.
I'm not too familiar with that drivetrain combo, are there seals on the output of the trans and the input of the t-case? If there are, there should be no fluid in that middle ground. If I remember right the stock setup has a little weep hole where the two meet so nothing can go between the two, only onto the ground.