I agree with Mac. A hardware synth like the Ketron will drop earlier-played notes in order to play the new ones if you reach its polyphony limit. I think you have a 128-note limit on the SD2 (check the manual).
There could be some MIDI notes hidden in tracks. Sonar doesn't always show all MIDI data, even in Event List View. Or, you might have a MIDI loop in your system, where played notes are looping back and triggering new notes.
Your MIDI file may have notes that have lost their "note-off" message, or on which the sustain is way too long. Again, Sonar won't alway show that info clearly. And, held or sticking notes may result if you cram too much data into your MIDI stream, in which case it may be your MIDI interface that is dropping the ball. Large amounts of CC data may also clog the stream.
Break your system down into its smallest components. Run only the MIDI playback app and one troublesome file, and see if you can narrow down what's happening. MidiOx is a great tool for finding rogue MIDI data floating around your system.
Theres' more, but this will get you started, I hope.
