I've just found the same problem in my NAS. Configured with 4TB of space, I was running out as I had 80GB left only, so I moved to an external drive almos 600GB, but surprise! My nas reports just 100GB free after it.
WTF???
This is a serious problem and D-Link support, even they are really trying to help, the don't have a clue and ask you to format your disk...
I've solved the problem by searching the file system from command line. I first intalled funplug so I can remotely login using telnet. Once at that point, you run as admin, and in my case I've found in /mnt/HD/HD_a2/recycle/nobody 1.4TB!!!!!!!!!
So 1.4TB of data that I tought that I deleted, was really under a recycle bin of a non-existan user and can be safely deleted.
What really bothers me is that I bought an external 2TB drive to free up space in my nas, and now it turns out that my nas is really about 50% of it's capacity!
So, right now, I'm seriously thinking about selling a brand-new USB 3.0 external drive and a D-Link DNS320, to buy something that really works like a QNAP.