Many reasons, in some cases the retailer is selling the stock for the price they got it at, and other cards were purchased at a later date at a lower price and thus have a lower selling point. You can see this on newegg pretty regularly, an older out-dated thing will be selling for a higher price than the new hotness.
Additionally, from one company to the next, quality of components/company come into play, capacitors/pcb's/everything has different grade levels, to save money and increase profit some reference manufacturers use the very very bottom end, this results in a card more prone to failure (generally if you cool them very well its a non issue, but if you don't, they'll cook themselves quickly)
Example here being Gigabyte, yeah they offer cheap priced 5870's, but they are cheap, RMA's are a nightmare and generally you're getting what you pay for.
And last but not least: "just because". Weird pricing happens all the time