This is what I've heard from other people too. Your first entry on a new Visa has to be through normal (foreigners) channel, after that you can get it added to your GE profile. (Which is essentially what happened to OP, they couldn't use their new Visa with GE.)

When I signed up for GE I had to: (A) enter my Visa details as part of the GOES application and (B) the interviewer copied/checked the details and scanned the Visa during my interview. Since there's no way to edit the Visa in GOES that suggests an officer has to manually fix your record for you.

During my interview I asked about additional citizenships/passports (I'm currently undergoing naturalization in another country, so I might gain a new citizenship+passport in the next year or two), they told me I should just come to any GE enrollment center and they'd update it for me. I imagine its exactly the same for new Visas.

I'd recommend visiting a GE enrollment office the next time you're at an airport, they can probably add the Visa immediately / without an appointment. (I had to get my DOB corrected, and they did that without any waiting in SFO, took about 2-3 minutes to find my profile and edit it.)