We use Jenkins behind a firewall where we can't use Github event hooks, so we have a Github organisation project that periodically polls.
After a Jenkins upgrade, we found updates aren't triggering builds. The problem appears to be that after the organisation scan, it is no longer scanning the individual repositories in the organisation. We can see that the timestamps in the scan log for the organisation are recent but those for each individual repository are old. Manually triggering a repository scan has the desired effect.
I've set up a toy Jenkins installation and reproduced the problem with all-latest plugins. It seems to be a regression between branch-api 2.0.16 and 2.0.17: if I downgrade workflow-multibranch to 2.16 (to fix dependency problems) and switch branch-api between 2.0.16 and 2.0.17 then it works as desired with 2.0.16 but fails with 2.0.17.