Here is the issue that I see. When I record a series that doesn't have good metadata, we get the recordings each on it's own folder, and they are recognized as separate shows.
Give the show an internal number when a recorder series is created, to ensure that all of the series get recorded in the same folder. It kind of already behaves this way if the series has metadata, and it doesn't find the proper episode to match.
I don't expect Emby to create data that doesn't exist. But it should be smart enough, that when I select in recorded TV to record a series, it should be smart enough to group all recordings under one TV show.