Windows – Hard disk used space wrong

I'm having an issue here that, so it seems, many users have had. My used disk space on an internal disk is off. And not just by a few GB.

It's an external Western Digital backup drive. I use it for filehistory (in a Truecrypt virtual disk, so one big file) and just some storage.

The drive itself is 1TB. All my files together are about 386 GB. I have confirmed this with the program TreeSize. Yet, Windows tells me that I have used up 687 GB of the total 931 GB.

So the issue here is not that I have 931 GB instead of a thousand. The issue here is that Windows thinks I've used 687 GB of the 931 GB, while I have actually only used up 380 GB.

This is quite a lot of space I'm losing here. It could be that I never noticed it, but now I did and I'd like to fix it..

What I've checked so far:

• Shadow copies – Turned off
• Turned off indexing
• Tried the disk in an other system
• Checked if there was a hidden partition, but it's an actual full size partition
• Defragmented
• Removed Recylebin folder
• Checked with dir /a for hidden files or folder
• Used TreeSize for hidden files or folder, but this gave me the actual size, and the same "used" information as Windows explorer