Yosemite User Template not loading

I have 20 macs in a University lab imaged identically, with a user template I created. Worked well for several months. Lately, the chances that my user template does not load correctly is 50/50. This takes the form of:

• the dock loaded is generic and does not include my pre-selected apps
• the wallpaper is the default 'Yosemite' image and not the wallpaper I created
• or, mounted hard disks are not displayed on the desktop.

In the above photo, the bottom image is what I call an incorrect profile. It is in this profile you can see the dock, hard disk, and wallpaper are not loaded; however, things like Finder and Safari open to the correct, templated location.

I can log in and out of the same machine all day and come up with a 30-50% chance the template loads correctly. However, I need this number to be 99.9%

Our lab is partially controlled by JAMF/Casper to load scripts upon start-up. These log-in scripts take the form of:

• loading PHAROS printing client
• loading a 'university emergency alert' app in the dock
• if the user has a folder on our xsan server, Casper scripts mount that folder to the desktop (this feature works on our Mavericks stations, but is broken in Yosemite).

What process occurs when a user logs in and the template is pulled from? Is it possible that Casper log-in scripts could be conflicting with the user template creation?