I have the same problem, firmware update freezing after "Triggered a notification on Identify char". In my case bundle version is 201611070000 and bean version is 20160929.
It can see the bean, I could blink the LED, but firmware update always failed. I then tried to update the firmware using the android app, that tried twice and then reported failure. Since then I haven't been able to blink the LED either, it still connects to the bean but fails immediately after the "Turning LED on..." message.
Just tried renaming the bean which fails after "Renaming Bean to:" message, and spits out the same debug stuff as when it fails to blink.
This is on Windows 10 with a fresh install of all the bean tools (Saturday) as per the getting started guide.