It seems like you exported the MIDI incorrectly. Do not use the macro that converts all channels to MIDI Out. This is especially problematic if you use FL Studio for writing music, because you will lose all of your instruments.
You can export MIDI from a single pattern directly from the piano roll. This will preserve the state of your FL Studio project file, and allow you to export MIDIs for individual patterns at a time (such as for main melody and harmony, or for verses and choruses).