V5-0 - Input clamping diode not clamping
The I-V function of the Schottky diode D6 (HSMS-2802 - input clamping) is not steep enough to clamp the input to +3.3V. For example, when driving with 5 V pulses from a 50-ohm terminated source, the diode current is approx 30 mA resulting in a dropout of ~1.5 V - so the diode is not clamping the signal at all. On the other hand, Schottky diodes with steeper I-V function have higher junction capacitance.
The previous version of the board used a BAR66 RF PIN diode, which did clipping well but its' long recovery time (0.7 us) was causing spurious TDC events (see issue 515). A workaround in VHDL was provided for that purpose. Therefore, I recommend replacing D6 back with BAR66.