Server 2012r2 Home Folder

I started using the Profile tab for user's in Active Directory (2012r2) to map a network drive for the specific user.  We use to do this before by putting a login script in the startup folder on the client machines.  The login script would map the company network drives as well as each individual users drive on the server.  I have now started to use Group Policy to map our network drives, but needed a way to map individual user drives.  For this reason just used the AD Profile tab for these individual drives.  It works just fine but I had a user complain to my about his PowerShell when opened defaulting to this network user drive now.  I have also noticed that within the individual network user drives there is now a windows folder created automatically.  Is this the reason for the PowerShell issue?  Is there away around this?  Is there a way to set this so the windows directory is not created in the users network folder?