yea, it sounds like the boots may be to blame...heres my theory:

Even if the holes are small, it will make a difference. your feet are pretty much plugging the tops, so every time you shift your feet, move your toes, etc, a small quantity of air will enter/leave those holes. that air would likely carry a pretty large quantity of scent with it being from your feet (average feet perspire, and hence smell,almost as much as armpits).

thought about just patching them if you dont want to buy a new pair?...course then you have to worry about the scent of whatever product you use.