I'm sure there are others here that can explain it better, but it sounds like you had too wide of a lens on.
I don't normally suggest people go to Ken Rockwell for technical advice (insert your own KR joke here), but he sums it up in a way pretty easy to understand. There is a sample photo about half way down.
http://www.kenrockwell.com/tech/filters.htm
He says "The weird results on ultra-wide lenses are because the polarization of the sky varies from one end of the sky to the other. Polarization of the sky is maximum at 90 degrees from the sun, and none at the sun and 180 degrees from it. This is no issue with a tele lens, however with a super wide you are sweeping such a broad expanse that the polarizing effect will vary greatly across the sky. You often get a dark area in the sky, which usually looks nasty. I rarely use polarizers with ultra wide lenses."