I figured it out!
The games that I was trying to delete were disc installations that were done in the MS dash before I had F3. For some reason F3 won't delete the data from that path, it just removes the game cover from the Games tab, and after that the installation isn't visible in the MS dash either. So I found this HDD folder list: http://360.kingla.com/, and was able to find the undeleted data folders using the File Manager.
Games that were installed in F3 delete just fine from the Games tab.