I couldn't get data from dataviewer earlier, so I came over to the 40m to look at it here. Unfortunately the system here is down at the moment and Alberto is rebooting it just now.
I went in to take a look at the beat signal on a scope and the good news is that the clocks have now synced. I'll get back out here tomorrow some time to take some data. They are not at the zero-crossing point, but are sitting about 200mV off (500mV is pi radians of phase). I'll try to adjust this with some different lengths of BNC tomorrow.
Till I get proper read-out, here is a picture of the scope screen.