Input signal from other board measures an extra cycle wider on signaltap on Stratix 10 vs Cyclone 5

Hi, I am trying to interface the FTDI601 USB Bridge (https://ftdichip.com/products/ft601q-b/) to the Stratix 10 1SG10MHN3F74C2LG_U1/U2 FPGA on our design board. The reference clock for the interface...