All of the notes from the various instruments are being written to a single MIDI track.
You must be running intelliScore Ensemble Edition to create multi-track MIDI files.
In the New Project Wizard, at the What Instruments step, select I know what instruments comprise the original audio.
At the Specify Number of Different Instruments step, select Multiple.
At the Select Ensemble step, you can select, create, and/or edit a multi-instrument ensemble. You can click the Globe button to see the list of active instruments. After intelliScore creates the MIDI file, the file will contain one MIDI track for each instrument selected.