CapriUni, I've had several problems which may also be similar to what you're talking about.

Some midis are synthesized or "made" by playing a keyboard as opposed to entering the notes by hand (or mouse). These sound beautiful but are nearly impossible to understand by looking at the notation. Sometimes chords (notes that sound like they are played at the same time) are actually written as 16th or 32nd notes in different staves and with crazy rests. One arrangement of Amazing Grace I transcribed from this type of arrangement was extremely simple to play, but the notation was a jumble. I just had to listen to it instead of relying on the score. One thing that helped me with this particular one was to continually change the resolution in my midi software. Sometimes changing the snap helped, but not as much as the resolution.

As far as hearing the melody, I also found that some midis that aren't quality midis don't have a good balance (volume) between voices. I like to make the melody a little louder, also accents. I suspect that for some reason the same midi sounds different on my two different computers, speakers, etc. Just last night I was trying to write a midi for Holy Manna (a choral arrangement that has a beautiful countermelody). It is soooooo easy to play on the piano, but quite difficult to do all that phrasing electronically.

I looked at your Black-eyed Susan midi. Actually I think the midi is very clean and could not be written simpler. But then I love the traditional Irish manner of singing (with lots of grace notes), similar to the American Gospel-type where the singer hovers all around a note. One other suggestion is to use a midi search engine to find a particular midi you like (if it's available).