The windows have two functions to ensure they move to the correct position. Each window's position values are stored in their respective door module. Your Passenger Door Module (PDM) appears to be working. The Driver Door Module (DDM) is not storing the correct position value for whatever reason. Knowing how the windows are supposed to operate is the key to diagnosing a problem when they aren't.
The first window function is Normalization. The upper/top window travel limit is called the Zero Position. The DDM and PDM figure out the actual window position by comparing the positional feedback from the window motor to the Zero Position. Determining the Zero Position is the reason you raise the window to its fully-raised position and hold the switch to commit the position to the module in each door. If the window is being raised, and it stalls for any reason before it reaches the Zero Position, (like if your head gets in the way) that stalled position becomes the new Zero Position. This is called the Anti-Trap feature. Also, if power is lost from the battery and the door is open, the index position is erased and the position of the window at the time of power-up becomes the new Zero Position. The next time you open the door, it will index down (approx. 4 mm.)
Indexing is the other window function. When a door OPEN command is sent by the interior or exterior door switches to the respective door module, the window will drop approx. 4mm to clear the upper seal. When a door CLOSE command is issued, the window raises approx. 4mm.
Based on the symptoms you've described, your problem appears to be centered around the Normalization function on the driver's door side. It is most likely the Driver Door Module or a switch-related fault, but I'm troubleshooting this fault remotely, so I'm not omniscient. A chaffed wire, fouled connector contact, or loose ground could also be responsible.
As in all things XLR, adequate battery voltage is key. If the battery isn't fully charged, really weird symptoms appear. If your battery is fine, then disregard. But if in doubt, ensure it's fully charged. This is a nice feature of the Battery Tender, it indicates the battery status when it's connected, and has a permanently mounted, quick-disconnect cable so it's easy to plug in whenever needed, though it does come with alligator clips. The permanent cable is the way to go. You just tie-wrap the charging cable to the battery in place, and plug the charger cable into it with the hood unlatched.
Let's get back to your problem. Perform the same procedure, but leave the battery disconnected for thirty minutes, before Normalizing the windows. This is excessively long, but it's worth a shot. When you re-index the driver's side, hold the switch for ten seconds in each direction. (This is twenty times longer than necessary, but plenty long for the Class 2 bus to recognize the command and store to the DDM memory.) Report back with the results.
CC