This has happened before:
http://216.239.41.104/search?q=cache...rst+disc&hl=en
What I suggest is the following:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Servic es\Cdrom
Change the "Autorun" to 0.
I'm assuming you know what that long line of stuff above is and how to use regedit. You'll want to log out and then back in. This will set your CD drive(s) to never autorun. You can also right-click and go to Properties and then look at the Autoplay tab and set each one to take no action, but the registry change is the easiest, IMHO.
Why this happens: I personally think it's because when the windows shell tries to load the autorun.ini something hangs and it never finishes. Which is why external apps to the shell, like Windows Explorer and software that needs files on the CD drive, work. Meanwhile, the explorer shell itself doesn't know what is going on and might even still be trying to autorun.
There, an entire length of help and I didn't insult anyone. Aren't you fsckers proud?