I think the timeout has to do with direct communication with progress back to Backburner. If it doesn't hear anything it's listening for, then it assumes it needs a re-submit. Autodesk jobs work fine without setting the -timeout switch.
On Deadline it's a lot easier to manage. I remember seeing a progress line in the console of a networked render machine when I VNC'd to it, which I don't see from Backburner.