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It sounds like your client machines have the Interactive Services Detection service started.
Disabling the Interactive Services Detection service will prevent the popup. Though I've seen a handful of people do it with no apparent adverse effects, I don't know the full scope of what this service does within Windows, so disabling it is at your own risk.
- Open a run box and type services.msc
- In the Services window locate Interactive Services Detection, right click and choose Properties.
- In the Properties window Stop the service and set it to Manual or Disabled
- If the service starts again when it is set to Manual, try instead setting it to Disabled Interactive Services Detection Popups
If this corrects the problem, you could write a batch file to disable the service, or potentially look at if your x64 image had this service enabled when captured. If so, it may warrant recapturing with the service disabled.
Thanks for the response. This is what I believed to be the issue and as you mentioned its unclear on what this will affect if disabled so I have been reluctant to do so. I think I will look at disabling through GPO and start with a handful of machines and see if anyone shouts!