So another unsolved mystery.
Just my 2 cents. I always master my songs in a Wave editor and then I burn to CD and / or convert to MP3.
Sometimes because I forgot to use "Select None" before export I'll have a song that some tracks are missing from. If the last thing you edited is still focused ( highlighted in Sonar) then that sometimes is the only item that will be exported. So we need to use "select all" or better yet, "select none" I fine "select none" bullet proof.
I think the mistake your making is not checking your exports with either a wave editor or a media player.
Even if it's just a rough mix it's worth taking the time to also do a basic mastering before sending it off.