Hi raywill77,
when you are in "Song Creator - Tab Channel - Setup" screen, it is very important that the MIDI file's position is "at the beginning".
Therefore I recommend to press the SONG STOP button "as a precaution" (before pressing the "Execute" button and saving your new file).
Please control also the settings in "Setup" screen: The upper boxes (Voice to EQ) should be all CHECKED, the lower boxes should only be checked if needed. When "Keyboard Voice" is checked for example, the actual Voice settings of the Keyboard Parts will be written into the MIDI file (what will override your Voice settings stored in Registrations).
Best regards,
Chris