What kind of instrument were you using, and what interface. Was it VISA? In my experience, VISA generates an error once the communication timeout is reached. The timeout is set using propery nodes. If you're using VISA, was the timeout changed to something ridiculously large?
I've never seen LabVIEW completely freeze in the kind of situation you're describing, but then I wasn't using Linux, so I don't know if that's a factor.