Been looking at the clock output form PCB 8, not happy with what I'm seeing.
Looking at TP101, the clock signal is an approximate sinewave and I'm assuming this should be a 5v square feeding the hex inverter IC 430.
Now my very busy working week is over, I got some time to come here and catch up.
As others have said, it may simply be your 'scope making it look like that, but I'll have a probe of mine after dinner and post some screen captures. The raw clock output and the control inputs are kind of sensitive to being probed.
When I was looking at the clock on mine, I found that the very simple setup instructions in the manual of 'adjust L401 on PCB8 until TP402 reads 3.0V +/- 0.2V' to be woefully inadequate. For a start, you can't probe TP402, even with a X10 probe and expect the PLL to lock as the probe steals enough current to stop the PLL from locking. Instead, I removed PCB8, powered it from one of my bench supplies and then used a counter, with its timebase derived from a GPSDO to adjust the free running frequency of the oscillator to as close to 49.152MHz as I could get. That ensures that the frequency should be in the range that the PLL should be able to achieve a lock with.
I discovered how sensitive the clock control at TP402 was when I was trying to monitor TP403 and TP404 (the 50Hz from the mains and the 50Hz created by dividing down the 49.152MHz clock) while also monitoring TP402. The PLL never even got close to locking. When I removed the probe from TP402, it got much closer to a lock, but never actually achieved a stable lock. I'm guessing that either the varicap on PCB 8 or one of the other components is a bit 'tired'.
If you probe just TP403 and TP404, you can see if the PLL ever does achieve a lock. On mine, the leading edges of the signals cross slowly back and forth, but never actually align and stay there. It's almost as if the time constant for the PLL is wrong.
Oddly, when you look at the circuit diagram of the optional crystal oscillator, it doesn't even use the control signal from the PLL, which makes me wonder how important the lock to the mains frequency actually is. I tried feeding in a reasonably accurate 49.152MHz from a signal generator with PCB8 removed, but it did nothing to improve the approximately +/- 12μV of noise that I see on my 7061 when measuring on the 10V DC range with the inputs shorted.
Earlier this week, I had an order from Mouser arrive and part of that order was some 49.152MHz crystals, so I'll be making up an oscillator board that I can try as a replacement for PCB8. It won't be locked to the mains, but it should at least be fairly stable.