Even if this question might be too simple, but have you emptied all your recycle bins (like the Windows recycle bin, the Executive Software recycle bin, the Norton recycle bin, ...)? I know that the Norton recycle bin hides itself from Windows so you have no way of entering it with Windows (it's stupid, but you have to use some DOS program to change to the hidden directory and work with the files). This could be one possible solution.

"Normal" hidden files are an other possible source of your problem.

The next idea I could think of is a partition tool. Have you used one lately? I once used Paragon Partition Manager and when resizing my partition, it only resized my partition. It didn't care to make any changes to the NTFS file system. So I ended up in a 30 GB partition with 64 GB of free space and lost some files until I noticed the fatal error.

How does your "all seems to be twice" look like? Do you have all folders twice when you look at the in Windows Explorer?