Even if you can't fix it, there ought to be something you can do short of a re-boot. For instance you could try disabling and then re-enabling the drive. You can do that from Device Manager. One way to get to device manager is: right click on My Computer. Click Manage > Device Manager (under System Tools).
Here's one thing to try. When you eject the first disk, do it from Windows Explorer. Right click on the drive, then click Eject. Supposedly when you insert the second disk, it will refresh.
You can also play around with "Auto Play" if you haven't tried it yet. Right click on the drive. Click Properties > AutoPlay tab.
If you've installed some CD burning software, maybe that's the problem
If you have XP Pro, DougKnox has a tip that enables you to control AutoPlay, even for external hard drives. When I plugged in my external hard drive with 4 partitions, XP used to start up multiple copies of AutoPlay faster than I could kill them. Not anymore:
http://dougknox.com/xp/tips/cd_autoplay_pro.htm
I suppose it could be the fault of the driver for your CD drive. CD drives are cheap these days. Even DVD/CD burners.