Ok, so I have managed to find the reason why this was occurring, or at least got it to stop.
I have set up Advanced Endpoint Assessment ver. 3.6.1177.2 - Host Scan, under Secure Desktop Manager.
After removing all Microsoft products from all 3 options:
AntiVirus, Personal Firewall and AntiSpyware.
The pop up of Windows Defender then went away.
This Host Scan was working fine for a couple of months, so I assume Microsoft changed something in Windows Defender, which causes interference with the Host Scan.
Is this something that needs to be updated in Cisco Anyconnect, or Windows 10?
I am running Anyconnect v. 4.6.01103.
We don't actually use Windows Defender for any of these products, utilising ESET Smart Security for AV, FW and AS.
So do I need Host Scan checking for all these scanners, I figured I do, for when someone connects using their non work PC which could have whatever AV installed.
Thanks,
Tim