Hello Jerry,
Welcome to the forum, and many thanks for the interest in Hauptwerk.
Are you trying to use Hauptwerk's built-in MIDI recorder/player to play the MIDI files? Or an external/VST/AU MIDI sequencer application?
Were the MIDI files in question recorder with Hauptwerk's built-in MIDI recorder/player, and with the same sample set (organ)?
Hauptwerk's built-in MIDI recorder/player uses a special MIDI implementation that's fixed for each individual organ, which you can view using the 'Recording | View MIDI recorder/player/sequencer MIDI implementation (for this organ)' menu function. For background information on that have a read through the 'MIDI sequencing, the Hauptwerk AU/VST Link and applying real-time reverb' section in the Hauptwerk user guide (on the Help menu in Hauptwerk; pages 181-199 in the current v4.1.1 version).
Hence if you want to use Hauptwerk's built-in MIDI-player to play a MIDI that wasn't recorded by Hauptwerk, or one that was recorded using a different organ in Hauptwerk, then you might need to edit the MIDI file using a MIDI sequencer in order to change the MIDI channels (etc.) used within the MIDI file so that they match those detailed by the 'Recording | View MIDI recorder/player/sequencer MIDI implementation (for this organ)' menu function, so that the notes in the MIDI file play on the intended virtual keyboards.
Alternatively, you could use a MIDI sequencer application to play the MIDI file through Hauptwerk (e.g. via the Hauptwerk AU/VST Link, with the Hauptwerk AU/VST Link selected as a port in the left-hand 'Console MIDI IN' column on Hauptwerk's 'General settings | MIDI ports | MIDI IN ports' screen), and manually configure the MIDI implementation/channels for the virtual keyboards in Hauptwerk to match those used within the MIDI file.