Windows 2003 Server

I recently upgraded a WIndows 2000 Server (Standard Edition) to Windows 2003 R2 Server. The upgrade process went very smoothly but now when I try to install an application I receive a message that another installation needs to reboot the server. I have rebooted several times to clear this but to no avail. I also tried looking this up on the Microsoft website but they didn't have anything (that I saw).
Any ideas as to where in the registry I would need to look to get this cleaned up?