Same Issue at BWI
I've had this similar issue within the last few months at BWI after OLCI. When I try to give them my nexus card at the gate for document verification they insist on seeing a Passport now. They told me something about a software change a few months back (who knows if it is true or not).
At DCA I used my nexus card all the time but I have not flown through there recently. I will have to try next time and report back.
It doesn't make much sense as Air Canada allows you to enter your Nexus information for APIS instead of a Passport. You think that is the information the gate agent would be looking for.