Hazarding a guess here. I believe the VLAN info for a switch is discovered only during an update of the Inventory. This is done in "Config" and then "Jobs". You can either create a new job, or edit an existing one that is an "Update Inventory" job.
The important part of all this is in the "Job Specific Details" when you're editing or adding a job. At this point you need to make sure the "Bridge Table" is checked, I think by default it isn't.
Try that and run the job and lets see if you get NCM to have the correct VLANs...