Recently updated Jenkins and all available plugins, and the Repository folder within our Organization folder stopped scanning completely. 

I went so far as to delete our entire organization structure and re-create it. The organization does scan correctly on changes. The only time the repository level folder scans automatically is upon its initial creation from the creation of the organization. 

Also makes little sense that the repository folder has a non-configurable interval of 1 day, while the organization folder was setup with an interval of 5 minutes. This is how the repo's trigger is defined in its config.xml:

<spec>H H * * *</spec>
<interval>86400000</interval>

I manually changed that to match the Org folders config trigger, e.g. 

<spec>H/12 * * * *</spec>
<interval>300000</interval>

and then gave Jenkins a restart. After ~5 minutes, sure enough, it's now scanning correctly. 

So why on earth is the interval timer being set to such a long duration, and so dramatically different than the org's interval timer?