I have configured my 2012 RD Connection Broker with a Thawte externally trusted certificate for RD Connection Broker Publishing. This is a trusted certificate for the client connecting all the way through the web access, gateway, connection broker and session host.
Whenever a user launches a RemoteApp from the web access, the prompt displays stating:
"A website is trying to run a RemoteApp program. Make sure that you trust the publisher before you connect to run the program."
Any way I can get the prompt to NOT appear without touching the client?