The AD9653 in question has a 100MHz AC coupled LVPECL reference clock (CK+/CLK-) similar to Figure 64 in AD9653 Datasheet.
The main difference is the PECL driver manufacturer and termination resistors (150R to GND).
The IBIS and measured results match showing a 900mV common mode voltage and approx 1000mVpk-pk input at the AD9653.
The AD9653 is connect to a PGA from a different manufacturer. The 100MHz AD9653 reference clock fundamental and
harmonics can be observed on the AD9653 VIN+/- inputs / PGA outputs. The 100MHz fundamental and harmonics are not on
the PGA inputs, PGA power supply or even AD9653 power supply. Powering down the PGA has no affect. Powering down the AD9653
by writing to SPI register fixes the issue. The magnitude of the fundamental and harmonics are essentially the same when
measured on the CLK+/CLK- or VIN+/-. There is no coupling mechanism on the PCB.
Any thoughts would be welcome.