My observation is that obviously some software and some of the flash data transfer succeeds. I believe your methods are correct, and so issues are either software or hardware. The one time partial increase in how far it gets likely means the eMMC at the location of the previous stall works, although I wouldn’t guarantee 100%…but it has worked at least once. Then it stalled at a different place, not much further ahead. You’ve tried with a clean install and with an alternate version install…I’m thinking it isn’t software either, although there is no smoking gun to prove that.
I’m leaning towards either the USB communications being at fault, or something within the Jetson hardware. USB communications issues are actually somewhat common, although normally associated with the host, especially if the host is a VM. On rare occasion a different non-VM host fixes something like this…or in the case of a VM host, changing USB setup. I don’t know what your situation is so far as ability to try a different host, but provide more details on your current host…Linux version, any USB HUB in the chain of USB cabling, so on. Consider direct attachment of the micro-B USB cable from Jetson direct to host with nothing intervening. Consider using a live CD type Ubuntu which mounts the original hard drive in order to perform the flash if you want to try a different Ubuntu version which does not require permanent install. If you want to try installing with the simplest command line you could try a live CD of something like Fedora 23 (Fedora can’t use JetPack, but you can “sudo ./flash.sh -S 14580MiB jetson-tx1 mmcblk0p1”). You’d be isolating results of how hardware behaves using alternate operating system versions. Use a different micro-B USB cable if available (it usually is not the cable, but most devices these days come with an OTG port, and type micro-B USB cable, so chances are you have a spare somewhere).
It could also be the Jetson. It might be time to RMA, but if it turns out to be a host issue, then you’re back to the same problem. If the issue is something simple like the USB cable or HUB, it’s a big consumption/waste of time for something otherwise quick to fix. So testing the host itself, though requiring time, might be the shortest “predictable” route to go. If you had a second Jetson, then swapping it out for flash test would be instant knowledge of what goes wrong, but RMA and shipping isn’t as fast as testing host issues first.