That is strange. I have been watching some flights and usually CO's website had been cheaper, but only negligibly - like $5 on a ticket - not enough to really matter. There was one time, though, that if you booked a ticket EWR-HNL it was like $1200 a ticket on CO's website, but if you used the air+hotel package on Expedia, it was $1500 for TWO tickets including the hotel stay! My friend took advantage of that deal. I have only seen price differences if they were in packages, so this may be somthing new.
I prefer expedia simply because I do not have to log in to see a price. Sometime travelocity requires it (some links, like "Dream Maps" do not). I hate to divulge demographic info, so I created a fake user on travelocity and use it to check prices. Should I ever buy from them, I will then create a valid account.