To the original poster: if you are a frequent traveler to Canada, you should consider applying for Nexus. If you are approved for Global Entry, you're already pre-approved for Nexus by US authorities; you only need to be interviewed by Canadian authorities. Once approved (i.e., personal interview and iris scan), you receive a Nexus card in the mail.

If you are flying to Canada from the US, you use Nexus to clear immigration. When flying to the US from Canada, you also use a Nexus kiosk to clear US CBP. As far as I know, US Global Entry does not work at US pre-clearance stations in Canada because Nexus, not Global Entry, kiosks are installed at these stations.

The Nexus/crew priority line that you speak of is for Nexus travelers when the machines are not working. It is not for US Global Entry passengers because GE uses a different system (fingerprints) from Nexus (iris scan). I won't be surprised if the Canadian customs officer may have thought that you were a Nexus card holder.