I don't know if you've all figured things out, but I was able to solve my problem after calling Canon tech support. A process was running when I started my computer that was interfering with the CameraWindow program. I ran MSConfig, chose "Selective Startup," and then unchecked "Load Startup Items." I restarted, and CameraWindow worked. After doing this, you can run MSConfig again, and click on the rightmost tab, "Startup." Check one process at a time, click apply, then restart your computer. The process that was interfering with my camera was dlbkbmgr, which is somehow related to my printer.

Hope this helps!