The affidavit the FBI filed makes a pretty strong case that they were the same person. It seems likely the multiple DPR idea was an attempt to cover tracks.
He has put his name on two previous papers that use similar methods to link bitcoin transactions and identify entities or individuals
The first paper seemed to contain some very basic misunderstandings of how bitcoin works, such as apparently mistaking the private company Blockchain.info for the Bitcoin blockchain itself. There were also other issues claimed - I don't recall the details. Adi Shamir responded to most of these claims, though he never explained the bizarre confusion over the Blockchain itself, and I think you can find some of that discussion on Bitcointalk.org if you search.
The second paper attracted a lot of attention because it identified an address used to move a large amount of money by Satoshi Nakamoto and linked that address to the Silk Road, with the clear insinuation that Satoshi Nakamoto was intimately connected to the Silk Road. However, simply Googling the address in question showed that it belonged to Dustin Tramell, who confirmed that it was his. In reality, there was no link to Satoshi Nakamoto. Adi Shamir withdrew that claim, and attempted to downplay the issue by laying the blame for sensationalizing it on others.
This appears to be unrelated. The previous paper was trying to link Satoshi and DPR. This just talks about how DPR used wallets, and makes the case that the FBI didn't seize everything.
The paper that was refuted claimed DPR was linked to Satoshi Nakamoto, this paper traces the path of the bitcoins seized by the FBI and provides an estimate of how many bitcoin remain in DPR's possession.
A bit off-topic but I'm just wondering what this type of writing is? Is this a white paper? I really like the format they use and was wondering how I could write something like this.
Margins large enough to (fit a morbidly obese elephant / not pose a safety hazard to small children / summon Fermat back from the dead)? Yep, it's LaTeX.
The standard LaTeX classes (page styles) are really meant for books and such where generous margins are a good thing. See the IEEE journal paper LaTeX template [1] for an example of space-constrained LaTeX typesetting.
Yeah, most people who use LaTeX heavily get around to memorizing the \addtolength credo (or an alternative) fairly quickly. But the "holy shit, MARGINS" test has a very low false-positive rate in my experience. If you see !!!MARGINS!!!, it's probably LaTeX.