Are you using the iPod outside *in* the cold? Or do you mean just *when* it's cold outside. If it's actually *in* the cold, then there could be some physical reason. Maybe a prelude to those fancy-pants liquid nitrogen treated frozen speaker wires that some purveyors sell.
But if you just mean *when* it's cold out, and you're using the iPod inside a heated space, then I think it's just in your head. Well, I guess it's all in your head, regardless.
I wouldn't think that atmospheric conditions could make a difference to the sound waves themselves in this scenario. There's just so little atmosphere between the headphones and your eardrums. And most of that distance is inside your head anyway, all of it if you're using IEM's. Whatever space the sound is traveling through is going to quickly warm to near body temp & humidity anyway.
Certainly, atmospheric conditions affect sounds over a distance. The scenario of hearing better in the woods on a cool autumn morning is likely caused by temperature differences. If there is enough of a temperature difference between the woods and the atmosphere above, or even between the spaces within the woods, sound will react to those different densities. I'd suspect that it would cause sounds to be more readily reflected around within the spaces. So like being in an echoey room, things seem louder. And later in the afternoon as the temperatures equalize, there's less of a trapping affect. Sort of like how WWII submarines would hide from destroyers under different thermal layers of the ocean.
But yes, cold definitely can mechanically affect speakers. But not in a good way, in my experience. The easiest way to observe this is in a car if it sits out in the cold. On a bitterly cold day, the speakers will often sound tinny and distorted until the car warms up a bit. It's especially noticeable with speakers that have rubber surrounds.
Randy might be on to something. The cold, dry air of winter will dry out your sinuses. And since ears are part of the whole mucus-and-earwax network in your head, it could just be that your hearing is a bit better when your head's dried out.
Interesting topic. I look forward to hearing what other's have to say about it.