So after systematically eliminating one folder at a time, I found the culprit. It was a system backup (Not a system restore) file that i had set up about 2 years ago. Apparently it automatically backs up some files in my primary hard drive. The backup only shows up as a single file and it has multiple backups stored inside it. The icon is a small HDD with a disc in one corner and a green arrow in the other corner. If you try to right click the file and go properties, it reports being 0 bytes with 0 files and 0 folders.
To get the true size of this file, i had to go to "Start Menu" typed in "Backup and Restore" and click the program that shows up. In that window, it will show the location of the backup and the size of the backup file.
I still do not understand why this file does not report its size when right clicked. It was also missed by WinDirStats. Anyone know if this is as intended or if this is a glitch on my system?