I was using the updated content browser and upgraded from linux without a problem. The content browser doesn't have any effect on the update process, because that is checked before the OS has started.
Try to download a different version of the firmware from here:
http://updates.irexnet.com/embedded/dr1000/
Format the SD card, extract the files, insert, and press the reset button on the device. This should update your device no matter what state it's in.