Vortex Install Path issue

[UberPlaysSkyrim]

Uninstalled NMM, cleared the old mods, downloaded vortex. I open vortex and scan for my games. I have: The Witcher 3, Skyrim, and Fallout 4. Bunch of error messages, the biggest one is the hardlink thing.

 

Activate FO4, set install path to E:\Vortexmods\{Game}. This is the same drive as the game is installed in. Creates a folder called fallout4 in my Vortexmods folder, works fine. Check in file explorer and it's set to E:\Vortexmods\fallout4.

 

I activate Skyrim, set the install path to E:\Vortexmods\{Game}. I get the message "Vortex needs to access "E:\Vortexmods\skyrim\skyrim" but it's open in another application. The only things open are vortex and Mozilla. I open file explorer and find that the fallout folder is now at E:\Vortexmods\skyrim\fallout4. Nothing else is in the E:\Vortexmods\skyrim\ folder. Delete everything so that the Vortexmods folder is empty and try to set the install path to E:\Vortexmods\{Game} and get the same error message, only now the skyrim folder is empty.

 

Running Windows 10, games were installed off of steam. Any help or solutions would be appreciated.