Alastair found that the foam hut that he and Jan put on top of the Rb clocks to temperature stabilize them was too good of an insulator. The Rb boxes had gotten very hot and became internally unlocked as seen on the front panel.
After we let them cool down with the box off, I turned them back on. After several minutes the 'Locked' light came back on. Some minutes after that the '1PPS Sync' light also came on, indicating that the two had become somewhat synchronized. It really means that the frequencies are kind of close: I think its roughly that f1-f2 < 2 mHz.
I put the yellow box back on and have left it with a small gap on the bottom so that the hot air can get out. Hopefully, this will protect the clocks from the wind, but not cause them to overheat.
The signal going to the DAQ right now is DC-coupled, with a gain of 1. The peak-peak beat signal in this situation is 6300 counts.
My guess is that the clocks will by synchronized by tomorrow afternoon so that we can get the measurement done. Please don't disturb the clocks or the yellow box around them. Try to minimize any activity around that area.