This looks like small ommission on developers end but it brings problems if secondary location is enabled. TV shows are placed in subdirectories reflecting show's name but "Magnum P.I." is put in folder "Magnum P.I" and that path is in database which makes my Hazel crazy 
Could you correct this?
It does this for all programs that end with . (period). If you need to automate something, have your scripts truncate a trailing . to match what Channels has. Something like s/\(.*\)\.$/\1/ ought to achieve results.