Due to a problem in the Quartus® Prime Standard Edition Software version 23.1 and earlier, you might see that the input register is not registered in the ALTLVDS_RX megafunction's negative input pins, rx_in[*](n).
This is because the synthesis attributes "LVDS_RX_REGISTER=LOW" and "LVDS_RX_REGISTER=HIGH" are not assigned to the register in the Low-voltage differential signaling (LVDS) receiver interfaces.
To work around the problem, add the following assignments in the Quartus® Settings File (.qsf):
set_instance_assignment -name LVDS_RX_REGISTER LOW -to "altlvds_rx:ALTLVDS_RX_component|altlvdsrx_lvds_rx:auto_generated|altlvdsrx_lvds_ddio_in:ddio_in|ddio_l_reg"
set_instance_assignment -name LVDS_RX_REGISTER HIGH -to "altlvds_rx:ALTLVDS_RX_component|altlvdsrx_lvds_rx:auto_generated|altlvdsrx_lvds_ddio_in:ddio_in|ddio_h_reg"
This problem is currently scheduled to be fixed in a future release of the Quartus® Prime Standard Edition Software.