I'm flying to Puerto Rico in a bit so I won't be around for a while. I am going to dump all of the tips I have for this out here, I hope this helps get you going.
Try using win32diskimager release r15 available here.
https://launchpad.net/win32-image-writer/0.1/0.1
Also make sure you have your card in an SD adapter and in the SD slot of your computer or in a USB SD reader. You can't use you nook plugged in via USB for this.
If you are on Windows 7 right click on win32diskimager and select run as administrator. You should also make sure any other software accessing the SD card, such as my computer, is closed.
Here is another set of instructions that are more detailed, but they are written for a MAC. It's a good overview of the process though.
http://glasskeys.com/2011/06/27/how...-card-running-cyanogenmod-for-the-nook-color/
One last tip, don't try to flash the google apps zip at the same time as Cyanogenmod. I can't ever get that to work right with this installer. After you have written the image and copied cyanogenmod boot the device up and play with it. Then take the card out and copy the google apps zip file to it and reboot into recovery mode.
To reboot into recovery mode let the nook boot normally with the card in it then from desktop hold power key until a poweroff menu appears, In the poweroff menu choose "reboot", in the next menu choose "recovery" and press "OK". The nook would reboot straight into recovery.
It will install the google apps file in recovery then shut down or reboot.