Cisco mentions the Rufus installer, and perhaps in the past might have mentioned others. I don't know which one is applicable these days for ISE 3.1 and SNS 36xx - but either way, have you checked the ISO checksum to ensure the file downloaded correctly?
And try the rufus installer to see if it's any better.
Even once the USB has been created, you still have to edit a file, as described in the Cisco documentation - it has to do with how the USB is detected in the UCS server - without this mod, the USB won't start the ISE installer.