Yes got it working. So created a batch file called OnConnect_login.bat and saved it to %ALLUSERSPROFILE%\Cisco\Cisco AnyConnect Secure Mobility Client\Script
Basically anything starting with OnConnect will be executed from the directory if the run script option is enabled in the profile - Profile Editor / Preferences (Part 2) / Enable Scripting.
I uploaded the new profile to the AnyConnect section on the dashboard so it will be pulled down when the users connect next.
In my batch file I had the following calling the logon.bat from the logon server.
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@echo off
rem logon script for AnyConnect users
call %logonserver%\netlogon\logon.bat
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