I’ve been having this problem for a while now. I first noticed it with my web browser and since I’ve realised it extends to every flatpak I have installed. The regular versions are working fine, but as soon as I try running a flatpak, I’m able to give them the permissions for it, and can send them, but they don’t appear anywhere.
Following advices I saw elsewhere, I tried installing the “ASHPD Demo” app for testing flatpak portals and it has the exact same issue.
I also tried enabling the logging and looking at what appeared in the journal but again, there wasn’t anything to tell my why notifications aren’t coming through. It’s like they’re just going into the void.