If the Pulse client is used in conjunction with 802.1x (Juniper EAP TTLS), does hostchecker runs during the login process or does it run after the desktop is loaded?
If Hostchecker "interferes" with the login process, is it possible to invoke hostchecker after the login is completed (using the Pulse client)?
Are you using machine authentication or user authentication because pulse can be invoked based on this & by selecting the option listed in connection established configuration available in Junos pulse connection set.
Please check Connection is established feild in IC admin GUI under Junos pulse connection store
Are you doing Machine authentication or User authentication ?
In IC for Pulse Config What is configured for option Connection is established: ?
I have configured the "Automatically when the machine starts. Connection is authenticated again at user login" in my pulse configuration as I do want to authenticate the machine and/or the user.
Assuming your machine authentication and User authentication maps to two different role, you could try adding the Host Check restriction as part User Authentication Role and see whether that resolves the issue for you.