Hey Peter, Sounds like you've hit the same issue as us. We've had a TAC ticket open since November but still not fixed. After a few false starts I believe TAC have found the issue and that's duplicate UID's within FortiClient. Initially we were blamed as FN thought we were deploying FC via an image but this isn't the case, we deploy FC using the EMS software creator so it would seem like an EMS bug, although they haven't confirmed this yet. We're not so bothered about the client being shown as 'Not Installed' in EMS but what continues to cause us real pain is the constant VPN disconnects as EMS keeps pushing the same profile to the client. Possibly using the default profile for all clients would help but this isn't an option for us. I'm a great fan of the FortiGate firewalls but this EMS ticket has been open for 7 months and currently no sign of a fix on the horizon. Not sure how long our business will tolerate constantly disconnecting (IPSec) VPN Connections.
If if helps here's the ticket number for the above ticket, might help you get some traction with support 1969466.
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