Check that the correct permissions are being used:
What privileges do I need to grant to the ArcGIS Server account?
The ArcGIS for Server installation grants privileges to the ArcGIS Server account to read and write to the installation directory and perform basic functions such as starting and stopping server processes. The ArcGIS Server account does not need to be in the Administrators group on any machine in your site. However, before you create your site, you should grant the ArcGIS Server account:
Read and write permissions to the location your server directories will be created. Keep in mind that you'll need to grant the ArcGIS Server account read and write permissions to any new server directories that you create after configuring your site.
Read and write permissions to the location where your configuration store will be created.
Read permissions to the directories containing the database connection files that you'll register with the server before publishing. If you'll be using Windows authentication instead of database authentication, you'll need to also grant the account write access.
Read permissions to the GIS data folders that you'll register with the server before publishing. If you allow the publishing process to copy your data to the server (see Copying data to the server automatically when publishing), the data is placed in your server directories where the ArcGIS Server account was already granted permissions. You do not have to apply any more permissions to your original server directories.