Hi Kyu,
I ended up probing directly at pin 47 on AD9517 which is the REF2 input and I am able to see the waveform on the scope.
I played around with different level setting and waveforms for the external reference signal.
The device is able to detect (but NOT lock) a square/sine wave 0 to 3V at 30.72MHz. Anything below 3V and it does not detect it. Now there is still an issue with the PLL lock. It doesn't lock when the external reference is selected (even though I have set it to the same frequency as the internal VCXO, 30.72MHz).
We own an FMC110 board which uses the same clock tree device (AD9517) and I believe the reference input is differential. The reference input on that board works perfectly.
Not sure what is happening here, could there be an issue because it is a single ended input on this board?