I think that it's normal for the car to be a little lower on one side with adjustables, because of driver weight and a few other factors. I think you might have to adjust the driver's side a little higher than the passenger side.
I believe I have the same problem, except not as severe. I think mine is about 3/8" -1/2" lower on one side in the rear. I have the Eibachs with the factory struts. Its hard to tell unless you have a horizontal plane in the background to see that the spoiler is not exactly horizontal. I believe it is lower on the drivers side (not sure).
You guys might want to check if the springs were put on the correct side to begin with. My MKIV sits even w/Eibachs, but it was like that when I bought it.
Reason I mention this is I had a '99 Tacoma that I put a Fabtech lift kit on. The shop initially put the coils on the wrong side, and I had the problem you mention. Not sure about Eibach, but Fabtech intentionally makes the driver's side coil firmer than the passenger side to compensate.