Almost certainly. The SMP client communicates between the four concurrent processes via IP connections. These go via the loopback adapter in the current network interface driver, as can be seen if you open the Activity Monitor. The network traffic level is scary. If the IP address is lost, even momentarily, that traffic will fail and the WU aborts.Frustrating. This could be my problem. I know this is only a beta, but... Well, whatever. I'm sure people on the F@H forums have complained about this plenty.
I have been trying to leave my MPB connected with an ethernet cable. On the occasions that I have disconnected, the airport card picks up a neighbour's signal almost immediately (I need a new wireless router). I wonder if those few seconds of disconnect are enough to interrupt the folding?
Basically, you can't disconnect the network interface while folding. You have to shut down before making any network reconfiguration.