I have the same problem (I was down to 1% free space on the c drive,while having 95% on F and 65% on E). I also found if I deleted files from one location, they would sometimes disappear from the other, as well, and I would have to fish them out of the recycle bin. It was explained to me by Microsoft tech support(though I didn't really comprehend it)that the duplicate files in certain locations contained small things (little elves?)which enable the same files in the other location to 'work properly.' I realize this information probably isn't terribly helpful to you, but at least you know you're not the only one with the problem.

I eagerly await more knowledgeable explanations from those who understand such things.