Theoretically, MidiNotate should play a .NOT files exactly the same way as another MIDI application would play (1) a MIDI file that was imported into MidiNotate to create the .NOT file, or (2) a MIDI file that was exported from MidiNotate's .NOT file. This is true, provided that MidiNotate and the other MIDI application play to the same MIDI device.
If there really is a difference in pitch, then there are some possible MIDI effects that would come into play, particularly pitch bend. If MidiNotate were to play the pitch bend, and the other MIDI application doesn't, or vica versa, then you'd hear a difference. Also, there is a special MIDI RPN (registered parameter number) that determines the sensitivity of pitch bend. Pitch bend sensitivity is rarely used in MIDI files, but perhaps it is in your 3 or 4 MIDI files. Perhaps one or the other of Composer and your other MIDI application is ignoring the pitch bend sensitivity.
To find out what special MIDI events might be effecting the pitch you hear, you might want to try out MidiNotate Composer Pro at www.notation.com/ComposerProBetaRelease.htm
It's MIDI event list window will show you the special pitch bend sensitivity RPN events, as well as all other types of MIDI events.