I know this is an old thread, but I wanted to add something in case anyone is still having, or has this issue in the future.
This problem is incredibly annoying, and counter-intuitive to a good workflow.
When you choose the option to "duplicate track" or "duplicate track (complete)", it carries the same command/info (?) over to the new track, and MIDI information coming in will go to both tracks. To get around this, create a new instrument track from the '+' icon each time you need one (or whatever keyboard command you have set up for a new track) , or have them already in a template (created separately). Then drag-and-drop your desired virtual instrument to that new track.
Things just need to be done separately, or Studio One will combine virtual instrument tracks. Maybe this is part of, or a consequence of its automatic routing feature(s).
There might be a way to disable this in advanced settings, but I'm, not aware of it.