The issues I experienced had to do with clean installs of AGS as well as upgrades. None of the installations were able to create the site. After a lot of tech support phone calls, and hours of different installs with other settings (i.e. arcgis account as local admin, reconfiguring the site, etc.) and what not, we tried using my own domain user (which is a local admin to the servers) to install the software.
Since my domain user worked, and since the ArcGIS user was an admin, we determined there was something going on with the domain users and perhaps policy rules.
The workaround to solve the problem was:
- give the ArcGIS user rights to the C and D drive (I use d drive for directories and config-store)
- login as the ArcGIS user (previously created as a local admin)
- ensure arcgis user could connect to the internet as sometimes it prompted me for a user and password to open an internet site (I am sure some policy or another)
- added the esri sites
- run the install as admin
I am sure a couple of these steps might have been overkill (i.e. full access to C and D drives), but just in case. This worked and I plan on continuing this path. Please, keep in mind that 10.2.2 did not need any additional steps, it installed without additional tweaking and without the ArcGIS user being a local admin.
Another solution could be to create an ArcGIS domain user with local admin rights. I chose not to go that route because we (GIS personnel) have more control over local users than domain users.