In a previous topic, I used the Application Isolation Environment feature in Citrix Presentation Server 4.0 to solve an issue where sites require different versions on the Java VM. A side effect of this was, however, that the application would take around 60 seconds to launch. Turns out the issue pops up on Windows Server 2003 Service Pack 1 and has to do with certificate autoenrollment. Essentially a 60 second delay is implemented to speed things up… Hmm, let ponder that for a second, accept it and move on. To relieve my application launch delay issue, I created the following registry key, the planets aligned, and all worked well.
Source: Certificate Autoenrollment in Windows Server 2003