Update
I got 49/50 files uploaded. When trying to restart the last download, my computer gave me a message that hard drive "R" was full. At first I thought I had a computer virus that was filling my HD with garbage data but I have Norton and Malwarebytes installed and they stay updated. I checked my boxcryptor_portable folder and found "R:\Programs\Boxcryptor_Portable\Boxcryptor\app\.boxcryptor-internals\cache\.u" had 229GB used. BC portable was made to run on a USB drive so I knew something was wrong. It seems like every time an upload would get to 100% and restart, like I stated in the post above, BC would write the file to its cache again without deleting the other file. My "R" HD was completely full and I was afraid to turn off my computer without deleting all the cache files to free up some space. Hope this helps in someway to fix the problem.
http://imgur.com/gXdEW73
http://imgur.com/ECIXvuW