My music contains several different instruments, but in the generated MIDI file, all I hear are piano and organ sounds. (Ensemble Edition only)
IntelliScore Ensemble can create multi-channel MIDI files depending on the instruments in the original audio, as well as their pitch ranges and position in the stereo image. In the New Project Wizard, by default the Example - Piano and Organ ensemble is selected, which assigns all detected notes to either piano or organ. You can change this clicking the folder button to select one of the predefined ensembles or clicking the globe button to create or edit your own ensemble.
If you have the Polyphonic Edition of intelliScore, consider upgrading to the Ensemble Edition of intelliScore. The Ensemble Edition is designed to support audio containing several instruments playing at the same time.