I have used a number of programs, including Sibelius, and have not found a satisfactory and foolproof way round this problem other than recording the actual playback from the music program, either recording direct from the sound card to a wav file or going throuhg the line out jack on the soundcard.
It is all to do with the compexity of the midi file, and the way it is stored and interpreted, along with the instruments (voices) used.
I would be very interested to hear of your further experiences.
Cheers