You know those low priority issues that you never notice not working until months later? You can chalk this issue up as one of those!
Just noticed, many months after upgrading from v16 to v17/v100/BuildXXXX, that the Folder Auto-Clean no longer functions...at all!
For example, all of our accounts are set with the default Folder Auto-Clean Rules to delete messages from the Junk E-Mail and Deleted Items folders aged 14 days or older, yet we have messages in both going back 7 months to when we upgraded. It wasn't until a significant number of our customers started getting automated System Messages about Disk Space Usage that we discovered tens of thousands of emails in each folder for every account. We also have Auto-Clean Rules to reduce the size of these directories from 100MB to 25MB which haven't been doing their job either (we had a couple sitting at 2.4GB and one at 4.8GB!).
Edit: On the chance that it was one of those things that might not have worked with pre-v17 data I tried deleting the Folder Auto-Clean Rules for a domain and re-entering them and saving. Still doesn't work even with new Rules made post-upgrade. Tried doing the same with the Global Folder Auto-Clean Rules but no dice.