Ok being a black pastel morph explains a lot.
If you look at genetic issues in ball python morphs and combos at http://www.owalreptiles.com/issues.php you will see that super black pastels and super cinnamons sometimes have a defect called a "duck bill".
In a single gene animal that carries the "duck bill" defect, I believe that the head is shaped just differently enough inside that the snake will "wheeze" or "whistle" when it breathes hard. I have a female that has done it for years, she's a proven breeder, and she's never been sick a day in her life. Normally you can't hear her breathe but if she's excited or stressed she squeaks. Also, I would never pair her to another black pastel or cinnamon because of her squeaking; I firmly believe any supers she produced would be duck billed.
In a nutshell I don't think your snake is sick, I think it just carries the "duck bill" gene. If you don't breed then it means nothing. If you do breed then don't pair it with another cinnamon or black pastel morph.
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