Is your iPad actually getting managed with the pre-stage? You can look in Settings -> About -> Device Management.
To me, it sounds like something is failing in the PreStage that causes the device enrollment to fail yet it doesn't keep you from bypassing the setup assistant.
What settings do you have enabled on the Prestage?
In JSS > Mobile Devices > PreStage enrollments >
Click on your enrollment profile, and in Options > General, Make sure that you have "Make MDM Profile Mandatory" and probably the "Supervise Devices" section. I say probably because most setups out there will want the devices Supervised.
Also make sure that while you're here, go into the "Scope" tab, and search for the device. Click Edit and check the boxes next to the device(s) that you need to enroll.
Are you doing the "Require Authentication" where the AD credentials have to be typed in?
Just in case - the iPads do have to go through the setup screen process until they get to the Home Screen for PreStage to be sure that its done since you can go into Settings > General to check that the MDM is on there.
Hope this helps
I'm assuming you're not using DEP through Apple since you didn't mention that. If you are then I've had plenty of experience with DEP/Prestage and JSS and am happy to give suggestions!
I am having problems with the name assignment. All configurations are in place as stated above, however, the name will not apply to the ipad. Naming Method is "List of Names", I have the enforce mobile device name checked...one name is listed.
The ipad has the supervision profile listed. On iOS8.