Thanks - Windows Explorer wasn't seeing the card or camera, but Lightroom imported the photos when I asked it too. I just need to configure it now to load when I put the card reader in, and then eject when the files are uploaded.
Thanks for the tip. Still don't understand why the EOS utility and ImageBrowser Ex stopped working though.
If you've downloaded the images off the card, I'd put it back into the camera and format it... the card's file allocation table may need to be re-written.