I think I've figured out my own issue, but I'm not sure whether or not it is a bug.

With the default post-processing configuration moving files to %(MonitoredFolder)\Processed\%(Subfolder) if there is no subfolder, it moves them to %(MonitoredFolder)\Processed as expected.

However, when things are set up this way it appears the "Delete after" option only applies to the contents of the subfolders and anything in the root level of the Processed folder are ignored.

When I went through each of my profiles and removed \%(Subfolder) from the routing paths, it almost immediately started applying the retention policies.

The problem I see wis that sometimes I might have files both in and out of subfolders; based on the current behavior subfolders would be cleaned up, but files outside of the subfolders would not.