Receiving events from one private repo works while another doesn't.

I'm having trouble making the notifications work for one of our repos. While one repo works fine, for the other I just don't receive any events. AFAICT everything should be same for both repos. They are both private repos from the same organization. I'm using the organization-wide webhook, not a repo-specific one. I can see the Webhook delivery on the GitHub side and everything looks fine to me, I get a HTTP 200 OK answer from the Webserver in both cases. Can you suggest any way of debugging this further? Except for #486 which would probably help here, any ideas?

The issue names no files or tests. Begin by comparing the GitHub organization-webhook deliveries and repository permissions for the two private repositories, then review the plugin's webhook handling entry point. Done means the difference is reproducible and the cause or a concrete debugging path is documented, with #486 considered as related context.