Another helpful response I found from someone who had a similar issue:
I had the same issue...my vents in my 97TJ would wander around when at highway speeds or under heavier engine load. Initially, the problem would only happen when I was accelerating or going above 70MPH, and the vents would shift up to the defrost. Then when I backed off the throttle some, it would go back to normal. At the time it was a minor annoyance. Then it got bad enough that even at idle, if the fan was above the first or second speed, the door would slam half way shut, and just make a whistling sound - never fully opening up the dash vents. All the other vent positions seemed to open and close fine, though even the floor vent would shift to defrost under load.
Fast forward about 5 years, and it had become such a pain that I disconnected the panel vent actuator from the plastic arm that moves the door, so I could just keep the panel vents open all the time. That was only semi-successful, because sometimes the pressure of the fan blowing would slam the door shut again, and I wold have NO airflow - not fun when you live in Florida. I would have to stop so I could get out and reach up under the dash to flip the lever by hand again.
So finally, i got serious about tracking down the problem. I had already replaced the vacuum line and check valve that connects to the manifold, figuring the check valve was letting my vacuum escape when under load. It didn't help, and that's when I disconnected the door from the actuator. Today, I went after the second most probable culprit, the vacuum reservoir under the battery tray. I couldn't find anything visually wrong, and pumping 20PSI of air into it, while holding it under water showed no signs of a leak. So i put all of that back together - you have to remove the battery and tray to get to the thing, and went and got a vacuum pump with a gauge on it. With that, I was able to test each component, and finally pinned the leak down to an actuator.
The system would hold all the vacuum until I placed the switch in the panel position, and then the pressure dropped quickly until it was empty. So i naturally thought it was the panel actuator or the line to it that had the leak, but both of those were fine when I isolated them. After checking each line from the plug at the back of the switch, i finally found the leak. It was the defrost actuator that had the leak - specifically the 'half open' side (the defrost actuator has a half open connector and a full open connector). The line to the actuator had no leak, so I just removed it and capped it for now. That means the defrost actuator will not close fully, It opens fully when on the defrost setting, and half open in all other settings. As soon as I can get an actuator I will swap it out.
Sorry for the long post, I just wanted to put my solution out there for others, because I know first hand how annoying and how much of a pain it is fix this problem, especially when you are just guessing at what to fix or replace. The moral of the story...Get yourself a handheld vacuum pump (I borrowed one from the local Auto Zone), and test all your connections. It only took me an hour or so to find the leak once I had the right tool. And the problem ended up being the absolute last thing I would have expected to be the issue. I might have gotten there, but not before replacing the reservoir, more lines, the panel actuator (since that was the position with the problem), etc.
Now, after at least 5 years, my HVAC is working great again, even at highway speeds going uphill!
