I installed the 1.01 upgrade and I no longer get a link-light on my switch for the port Empeg is plugged into. I downgraded to 1.0 and the link light came right back on.
You didn't, by any chance, happen to accidentally download the "Mark 1" version of the 1.01 upgrade and apply it to your Mark2, did you? That'd disable ethernet, probably.
No wait, that upgrade probably wouldn't have worked, they have checks in there for this sort of thing. Right?