Because they pull the data differently and don't necessarily provide the same results.
And neither pulls Southwest airlines, which is generally a low cost provider when looking at airfare.
But the biggest thing to do is always check out the site of which one you choose. Sometimes you can find better deals that way, other times a 3rd party like Orbitz may be cheaper as they get rooms in a block.
Lastly, sites like Priceline & Hotwire can provide great deals too. You have to deal with their limitations and there are other sites where people post the answers that they recieved when booking with them to give you an idea of what you may see also.
Travel pricing is very much like brothel pricing. Every day prices can and will change and the price someone else got is pretty much unimportant as long as you are happy with the prices you received!