My system I use 110 V to 36 V power brick (medical grade), and having hybrid cable which takes this 36 V and Ethernet and goes to the system.
I am testing the EFT as per 61000-4-4 (± 2 kV, 100 kHz repetition frequency) at 110 V AC input.
At 1 kV my system fails with communication error (Ethernet failure, loss of data).
This means, the transient signal at AC input, coupling to DC output of power supply and then to Ethernet through the cable? Is there a way I can check this or debug?
Medical grade supplies usually are designed for low leakage to ground so it's quite plausible it would let the EFT go through. Also to pass EFT it only need to keep working itself nobody says it can let the pulses thru.
In my opinion you are right on the spot. I'd check on the output DC cable with a capacitive arrangement (in a pinch foil around the wire would do) or with some heavily protected probe (you don't want some kV in your scope, right?).
As for mitigation you could try some MOVs and/or chokes on the DC output before it reaches the ethernet combo but check if your medical standard allows these things
