We suggest rebooting your printer and making sure that when you click on the tab 'Devices' in MakerBot Desktop that you select your printer listed under connected devices. You should see a little check mark or blue dot next to it. Once you see that, you can then update your firmware. If you still experience issues please reach out to us in support by e-mailing support(at)makerbot(dot)com.
Has anyone successfully completed this firmware update? When you did, did it change the displayed firmware on the machine itself? How long did it take? Mine seems to hang on the update, I'm trying over USB.