I don't want to delete my old answer, but after reading all the comments and thinking about it while cycling to work. I think this is a more accurate answer.
As the Mathemagician pointed out, no agreement to give each dwarf an equal share was ever mentioned in the books. It does seem very unlikely that Thorin was going to divide up the hoard that was his fathers and his father's fathers into 14 equal parts. No doubt he intended to claim the hoard as his and reward his followers and friends as he felt they deserved.
The special agreement with Bilbo was drawn up to convince him to leave his comfortable home behind and come with them to the mountain. His share was to be "one fourteenth share of total profits, if any".
By this, no doubt they were thinking of any profits they made on the journey to the mountain (such as the pot of gold coins they took from the trolls, Bert, William and Tom) or anything that he might be able to steal from the dragon. Even Gandalf didn't think they would end up killing the dragon and claiming the entire hoard.
"that is why I settled on Burglary."
As Gandalf put it, it was a chance for Bilbo to make his fortune.
"Very amusing for me, very good for you - and profitable too"
When they drew up his contract, they were probably thinking: at the least they'll have to offer him a fair share of anything he burgles from under the nose of a dragon.
So 13/14 of the treasure was officially Dain's (as Thorins cousin and heir to the treasure) and it stayed in the mountain. From this, Dain no doubt paid every one of the surviving companions with wealth and titles.
Bilbo took the Arkenstone as his 1/14, gave it to Bard. Bard agreed to trade it to Thorin for the 14th share in gold (wrought and un-wrought) and Dain honored the agreement of the dead.
So, that's how the treasure got divided.
(Also is anyone else really excited to see how Billy Connelly portrays Dain in the upcoming movie?)
Ok, I'll replying to Brians comment in here, because there's so much more space:
I do agree Thorin considered the Arken Stone at much higher than 1/14, and was happy to write off 1/14th of his hoard to buy back the stone. He probably would have given over half of it, if it was the only way he could get the stone back.
Here's the quote about him choosing his reward:
“Now I am a burglar indeed!” thought he. “But I suppose I must tell
the dwarves about it—some time. They did say I could pick and choose
my own share; and I think I would choose this, if they took all the
Here are his last words at the Gate, which he took back later.
"I am betrayed!" It was rightly guessed that I could not forbear to
redeem the Arkenstone, the treasure of my house. For it I will give
one fourteenth share of the hoard in silver and gold, setting aside
the gems; but that shall be accounted the promised share of this
traitor, and with that reward he shall depart, and you can divide it
as you will. He will get little enough, I doubt not. Take him, if you
wish him to live; and no friendship of mine goes with him."