So with your discovery of the 1GHz clock, what I was seeing on the CLK inputs to the 1NB4-5040 zoom capture chips was not making sense. I couldn't figure out why they would go to the trouble of creating a 1GHz clock just to divide it down. I assumed, wrongly, that each chip had its own PLL that somehow synced up to a slower incoming clock. Not so.
My error was that I wasn't looking for a higher speed clock, so I didn't have the scope set up right to see it, and certainly not using appropriate probes. The clocks run to read out the data, and that was not a surprise, but they also run at a much higher speed when capturing the samples. And, as I found out, in zoomChipSelTest, the entire capture interval is much shorter than normal mode, on the order of 2.5us, and very easy to miss if you weren't looking for it in the test cycle of over a second.
So, instead of trying to observe the clocks with a looping zoomChipSelTest in pv, I set the module to repeat a data capture under normal operation. And this time I used Tek P6245 1.5GHz active probes. The 1GHz clock is at the limit of the scope and close to that of the probes, so everything looks like a sine anyway, and a wobbly one at that due to the sin(x)/x interpolation. A much faster scope system is really needed to probe the CLK properly. (And before anyone says it, yes, I should also use shorter grounds.)
Here are a couple of screen shots of the zoom clock inputs while capturing data. As before, CLKA and CLKB are each a differential pair (zoom_clka+_clka-.png). When capturing, CLKA and CLKB are duplicates with no phase offsets (zoom_clka+_clkb+.png). The frequency changes with the inverse of the sample rate. A sample period of 0.5ns (the fastest) runs the CLK at 1GHz, so the chip must be capturing samples on the rising and falling edges.
This is a guess, but maybe CLKA is for one half of the chip and CLKB is the other half. There appear to be two groups of 8 sample inputs and maybe they wanted the chip to be able to capture at different rates with 8-bit granularity in other instruments.
The last screen shot (zoom_capture_readout.png) is one cycle of capture and data download in normal operation mode. The above 1GHz captures are taken during the first waveform interval in the beginning at the trigger marker.
Just puttin' it out there for comparison if anyone needs zoom clock info in the future.