When building a terminal server, don’t forget to uninstall IE Enhanced Security BEFORE you install terminal services on a Windows 2003 Server, especially if you plan to sysprep the server and image it. For some reason, if you don’t do this, certain keys are left behind in the registry and in the default profile user hive (ntuser.dat file) that cause issues. IEES is uninstalled, but new user profiles created on that server still have remnants and do not function as expected. Users may get the IEES pop-ups when visiting any site that is not in their trusted sites list and it seems to affect JavaScript execution privileges as well. Here is the Microsoft article that addresses this issue (http://support.microsoft.com/kb/)933991). The workaround if this has happened is to follow Method 4 and then rebuild the affected profiles. If Method 3 is followed, it doesn’t seem be a complete fix from our experience.