A power cycle would reset the USB. One interesting question is whether pulling and reseating the thumb drive, rather than power cycling, would also change the behaviour.
The WebUI update does almost nothing different from freenas-update -- freenas-update is a small wrapper around several functions, which are also what the WebUI does. The main difference is that the WebUI then calls shutdown, while you have to do that manually with the CLI -- but you could try doing
freenas-update -C /tmp/cache check && freenas-update -C /tmp/cache update && shutdown -r now
for similar timing.
The most likely thing I can think of is the thumb drive being flaky, and taking too long to respond after a USB reset happens as part of the boot.