Hi Kris,
First it is recommended to run a Check Disk. It can help show the correct size on volume.
I encountered 3 possible causes of this issue.
1. Check if it is caused by paging file.
2. Sometimes we will have some programs installed, which reserved certain size for their log or any data file.
3. By default we do not have permission to access some folders such as "System Volume Information" folder. Sometimes it is a large folder but will not be calculated because of the permission issue.
Here is a thread which is caused by Event log it will also not be calculated so disk space is missing from Properties of system volume:
Server 2008 R2 losing 2 GB of hard disk space per day
http://social.technet.microsoft.com/Forums/en-US/b9ea0208-0f28-4917-95ab-96a0686cdeb2/server-2008-r2-losing-2-gb-of-hard-disk-space-per-day?forum=wins
For further information, here is an article which provided detailed information about "missing disk space":
NTFS Misreports Free Space?
http://blogs.msdn.com/b/ntdebugging/archive/2008/07/03/ntfs-misreports-free-space.aspx
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