Troubleshoot rule filters and check for problems in filter setup
If you have the latest PRO v3.2 build and you want to understand how rules are run (when not running as a service, but from within the program's connect and download), then you can use the Tracing feature.
In the Global filters tab, check the enable the Rule Tracing checkbox, then you can run a normal Connect and Download. Once that completes, you can click the little Search icon next to Rule Tracing checkbox in the Global filters tab.
This will bring up a popup where you can check and see for any email, what kind of body/attachments were present, which files were downloaded and which rule matched or did not match for those files (either email body or attachment).