Windows update IE windows keep coming up

I have 2003 server r2 installed on 10 servers. I have windows to automatically download and install updates, but when i remote desktop into the machines after a few days, there are 12 or so IE windows that are stalled on the main page for updates that says custom or express install. How can i get it to download correctly and install so that everytime i log into any of the computers i won’t have to close 10-12 windows displaying Windows Update.