Thank you for your questions! I'm sorry about the delay in a response on this thread; I'm seeing it for the first time today. I asked our development team and got some answers for you.
When does this routine run? Is there a way to manually force the rule to run?
There's not currently a way to force the auto clean rule to trigger. Its thread should be always running in the background - looping through domains and users and doing the cleaning. Since it is always running, the folders should never have messages more than one day past the auto clean threshold.
Can we check the logs to see when they last ran or had an error?
Auto clean logging is not currently available, though our developers have this on their list of requested additions.
If your auto clean rules don't seem to be running, one thing to verify is that the folder name in the system auto clean rule exactly matches the one in the folder. Even a hyphen in one name while not in the other could cause the rule to not trigger.
However, if you've verified there are no discrepancies in the folder names, and you have messages past your auto clean threshold in the folder, I would encourage you to reach out to our Support Department for direct support. They can review your installation to determine if this is a bug in the software or an issue specific to your installation. If you'd like assistance reaching support, I'm happy to help.