Hello, I hope you are doing well.
Am I correct in thinking that the iMX8MPlus is looking for a sink resistance to drive the signals? If so, how can I make this work with the PTN3366 which requires these series capacitors?
It could be possible but it is strange since those capacitors are needed as is mentioned on datasheet.
Did you try to change equalizer settings?
Did you consider squelch function? Where IC only operates when input signal is above minimum threshold (VRX_DIFFp-p).
Best regards.