Sorry that I misunderstood--I have problems like that with my father too---

I do the same thing as you do, on occasion, and have had jumble problems as well(hope I understand what your talking about this time)--I usually open the MIDI file in my sequencer program, rather than in the notation program, so that each track(and, at least usually) comes up separately--if I am lucky, there will be one track that has the melody, one with bass, etc, and I can strip the rest off--then it is just a question of removing the repeats and dealing with the intros and solos--

I've had problems for a number of reasons, the main one is when it turns out that the sequencer has been sloppy or even faked the melody--the melody notes are often slight variations of what the melody really is, or the sequencer decided to be "creative" and stuck a lot of his/her(tho guys are usually the ones who do this) ornamentation--I have even run across files that have extra bars in the melody! Another thing that can happen is that the arranger/sequencer has the melody move around from one voice to another, and rather than simply changing the patch(from say trumpet to clarinet) on the melody track, they move the melody to a whole other track--The worst problem is when the arranger/sequencer is not a very precise musician, so that notes end before they should or there are extra notes in phrases, well, you know what I mean--

At lot of times, you can get what you need, but other times it is just too much work, and you might as well just work out the melody, one finger style, and create a file from scratch--

Your best bet is to try to work with files that have been created by someone who is a good musician and that is faithful to their original source material--Lesley Nelson, who does the Contemplator site, is one of the best that way, at least for traditional music, and when I am looking for a tune, I usually check her site first--The other people who contribute there are very good, as well-- I often take MIDI's from there and learn the tune by "following" on either the keyboard or the guitar--