Waitaminute...anyways, why do you think Skipper has a flat head?

Simply put, it's just part of who Skipper is. He hatched that way without there ever being any explainable reason or cause for his head shape.

As for why the animators decided to do it, however, I suspect it may be because they wanted Skipper to have a buzz-cut-type military look to better portray his role as a commando leader.

I totally noticed that, but thats one of Skipper's features that makes him unique......AND AWSOME!!!! Plus, he always has a plase to put his coffee mug! lol!

My theory is that, in his days in the militia, his Paranoia cap got screwed on too tight. The effects are evident in his mannerisms and flat head.

Maybe he used to be the bottom of the penguin stack. XD

NO! Wait! Wait! Wait! He was a breakdancer!!! yeah...

because he was playing cards upside down

I think his head shape also makes him different from Private. They have almost the same size, so they let him flat-headed to distinguish them at first sight. And Private get fatter.

I don't think there should be any big reason why Skipper has a flat head. He was hatched [not for real, but you get what I'm saying, I'm sure] that way. The creators just decided to make sure you can tell Skipper apart from the other penguins, I guess.

It is most probably from a fight with Doctor Blowhole, or one of Skippers other enemies. I consider it to be Blowhole as he is THE most known enemy. You see, in the episode 'Dr. Blowhole's Revenge' They fight, Skipper and Blowhole, and where another penguin's head would have been smashed off, Skipper's glides across Blowhole's moisturized skin.

Either that or its a fashionable haircut.
Although it is rounded off in the movies...

So people can joke about it and annoy him to the MAX!!!!

If I were in PoM, I know I would.