We've experienced the same flying out of YVR. We drive up from our U.S. residence and enter Canada with our NEXUS cards. At YVR we go through US Immigration pre-clearance and walk under the sign that literally reads "Welcome to the U.S.," only to be told by the AS GA that we must show our passports before we board our flight to SEA.

To add to the irony, once a line-guarding YVR employee didn't want to let us in the pre-clearance express lane unless we showed her our Global Entry cards. We've never had Global Entry cards (the information is embedded in our passports but the employee of course can't read that). How did we gain entry to the line? By showing her our NEXUS cards! You can't make this stuff up.

We're flying out of YVR for the first time in awhile early Jan 2, and we're resigned to showing our passports, and maybe our NEXUS cards too.