I'm in the process of migrating from our 9.5 SP3 core to 9.6 SP1 (side by side), our agents are at 9.5 SP1 so we are using our 9.5 core to push a 9.6 SP1 Advanced Agent via custom vulnerability.
The process itself works fine, older agents are detected, i can push the repair (manually at this stage as we are testing) and everything works once you step through the continue buttons and by the end of the process the client is reporting to the new core and working as you would expect.
I have created a specific scan and repair setting to be used when running the repair job:
General Settings - Show progress dialog: Never
Repair Options: Always Prompt User / User cannot defer or cancel action
Repair Options: Message - Custom message explaining what is happening, After timeout start the install after 10 minutes.
Reboot Options: Never reboot.
The idea is that users will receive a notice explaining the update is coming down, you can keep working and will be prompted to reboot at the end (from the 9.6 SP1 client default policy).
What i am finding however is that users a prompted to hit the "Start Now" button 4 times before it will actually go - You hit "Start Now" the window disappears and then comes back, repeat 3 times and it goes, i'm not sure why this would be the case? We do't have this issue with any other scan and repair jobs.