Specifically with the www versus non-www, you can put different content on each so it is not really a mistake for Google to index them separately. They try to combine similar pages, and sure they should try real hard when they find duplicate content on www and non-www, but sometimes they fail. A lot of sites have this problem with splitting their pagerank in two.
I don’t know php but you do have two duplicate pages indexed separately which is a bad thing. This may not be your fault, but it is occuring. One is PR5 and the other PR4.