This is a good question! It is challenging to answer your question without getting in to some technical details, but I hope I have made it simple to understand.
Putting it very briefly, each note in a MIDI file can have a track number, a channel number, and a program change number.
When Synthesia opens a MIDI file, it examines all the notes in the file. Any notes that have the same combination of track number, channel number, and program change number are considered a unique part to Synthesia. Each part shows up on the "Hands, Colors, and Instruments" screen as a separate block that lets you change the color, instrument sound, play mode, and mute status of that part.
The "MIDI Track Channels" setting should maybe be called something like the "Part Channels" setting. The setting does not have a direct relationship with MIDI file tracks, rather, it's related to Synthesia's internally-assigned "parts". The setting controls if Synthesia will give each part a unique channel:
- When the setting is set to "Use Orignal", Synthesia will send out MIDI messages with the channel numbers that are specified in the MIDI file.
- When the setting is set to "Force Unique", Synthesia will change the channel numbers so that each part gets a unique channel number.
In more complex MIDI files that use a program change message in the middle of a song, or that use the same channel number on multiple tracks, the "Force Unique" setting will assign unique channels to the parts Synthesia generates. This will also cause each channel to have only one program change number. If you need to move around to different points in the song, it might be less confusing to the MIDI output device if the program change messages for each channel are always the same program change number.
Example MIDI file: