@tiffanysimkins : in case you’re still struggling with this issue, after some tests recomended in other forum, I was able to locate the root of my problem. It was a plug in called ThickBox. Not sure if it will solve yours too, but if you have this plugin you might want to try and disble it to see if you get your file tree back. If not this one, maybe another plugin is causing it. What I did was disable all plugins except Download Manager, and then went on to activate them all back, one at a time, while checking which one would cause the file tree to disapear.
Hope this helps. Good luck!