If this is intermittent and only occurring after a reboot, I would guess that you are encountering some sort of race condition. I'm not saying this should happen, but solving it might not be worth too much effort.

Why are you rebooting the linux host after each failed test? If you really think test failures are doing bad things to the server, you could restart ssh after failed tests. Probably overkill, but should be much easier/faster than rebooting the host.