Recently, I had some trouble with my application published through UAG.
Indeed, the UAG portal was not showing all the application I have access – not always the same application were shown.
If I tried to access directly to the web application (such as My Site or Outlook Web Access), I had sometimes the error ‘You are not allowed to access this application’, if I tried to use the Remote Desktop, I always the error ‘Your computer can’t connect to the remote computer because authentication to the firewall failed due to missing firewall credentials’ or ‘To use this program or computer, first log on to the following Web site: <URL link>’. This last error has been referenced by Microsoft and is already solved with a hotfix (which is off course already installed as my UAG server is up to date)
As these errors occurred only on some machine, which were recently reinstalled, I thought this was due to this reinstallation. So I checked the IE settings between a problematic computer and a good one, and I noticed that the Internet Explorer Protected Mode was enabled on the problematic station. I disabled it et voilà, problem solved !!!