Alright so let me start by saying that I've looked high and low and tried all other fixes I've been able to find on TechNet and elsewhere and this problem still occurs. We have two Terminal Servers, one having the problem and one not having the problem. I cannot find any differences on them so I am here hoping someone else may have some answers. The core problem is that we have some Group Policy IE settings that will not apply to a user until they reset IE. After that they never have another problem with it. So, the server is Windows Server 2008 R2 Standard SP1 and we are using IE8 because of the some special medical software that requires it. IE ESC is turned off for both Standard and Administrative users on the server. I have tried turning it back on and then off and logging in with a brand new user; I tried turning it on, rebooting then turning it off, rebooting again and then logging in with another brand new user. I know that turning ESC on or off changes a registry key also, and I did verify that it is off per that registry key.
When a new user logs in and tries to access any webpage from Google to a site that is in the Trusted Sites list, they get the popup that says, "Content from the website listed below is being blocked by the Internet Explorer Enhanced Security Configuration" and then they're given the choice to check the box not to continue notifying them. While that does not continue notifying them, nothing we have set in Group Policy for IE - Trusted Sites, Trusted Sites Settings, Popup Blocker Settings - is set accordingly until IE is reset. I have tried using IE 32-bit, IE 64-bit and IE No Addons.
Again, we have two Terminal Servers that are set up seemingly identical but we're having this problem in one. Any help would be most appreciated.