I recently had a customer whose backup drive was full with windows server 2008 SBS server. I checked and the VHD file was under half of total space. I ran a CHKDSK and could not find he problem. Finally I checked the shadow copy and set the limit lower to get it to work. Here are the steps.
1. Right click on the drive and go to properties
2. Click on Shadow Copies Then Settings.
3. Change the Use Limit to something smaller. I went to the minimum and it freed up the space.