Originally Posted by Cal Learner

You've done a lot of trial and error testing, so this may lead nowhere. But my thought is what babymog said below: a slightly cocked driver side window. Try this. Run the window up all the way closed. Then lightly tap the window switch down just enough to unseat the glass, but not to move it down at all. That would be just enough to un-cock it in the guide rails and align it properly. Could be the answer.