Hi,
these 2 clock generators are pin to pin compatible, but PIN7 and PIN5 are different definitions.

--The clock generator can output 2-channel 100MHz clocks, one channel is for CPU side, the other is for M.2 connector.
--The clock generator doesn't need linux driver, default configuration is OK.
So now you can measure whether 100MHz clock OUPUT or not.
According to your description, obviously, CPU side doesn't get the clock input or bad clock waveform.
Have a nice day!
B.R,
weidong