I assume so - the instructions weren't really clear. I used the pads where the screws mount the PCB to the chassis as my earth which seems to yield good, consistent readings.
I've since realised that I had AD843 op amps installed instead of the stock OPA604s though. New readings are much closer to 10mV, but still a little high and higher on one pair than the other (ranging from 11-12mV up to around 14mV on the higher pair).
I think it was in this thread that someone said Matrix says do not roll Op Amps.
I suppose we can see why they said that!
Sounds like they have got you to measure DC offset at the headphone outputs?