ssh keys and logins do work the same way regardless of TK1 or TX1, but since I can’t use JetPack with my host there isn’t a lot I can do to see what it is if you refer to something from JetPack or what JetPack configures. If ssh permissions are not correct, then the issue is unrelated to whether it is a Jetson, whether it is Ubuntu, or Fedora. JetPack does set up networking, so JetPack has an influence on this…but understand that ssh keys are generated in an installation, and that if your keys change, this is a problem. Each flash the keys will probably change.
There is also the problem that error messages may be overly cryptic. Supposing you need sudo to run a command, but you haven’t enabled the mechanism for a password popup (the ssh “askpass” mechanism)…you could see a message like above, it would be because you didn’t enter a password (with no popup, you couldn’t enter a password…you’d never even know it asked for one). Or files themselves could be invalid permission. Maybe you’re executing GPU code requiring membership in group video, but not actually in that group…you’d get the same error message.
A lot more information is needed on exact steps. I can’t use the JetPack instructions because I can’t use JetPack (and have a Fedora host). What was the command which led to the error? Has the board been flashed before? Does command line ssh work? Can your user execute or run some part of the command without nsight?