This doesn't seem to be a flaw in the calculation method. What Ripple follows is a way to keep the market circulation good without funds getting accumulated, other than what is kept as reserve in the Ripple Lockdown and for the founders. This can be considered same as that we have mining with bitcoin. We've got a total of twenty one million. Among them the entire volume isn't mined.
The following mining process is being done through the Lockdown and release of funds into the market at certain time period. If the entire volume gets released to the market the value will collapse. Just think the present scenario with the entire volume into circulation. The value will fall off.
Bitcoin also has its fair share of coins that are being kept in cold storage. So I don't think that this is something unique with Ripple. But what doesn't seem right is the fact that the co-founders and the promoters are holding a huge pie of all the XRP tokens in circulation. This is not the case with Bitcoin, or with other altcoins such as Ethereum or Litecoin.
And it is not just Chris Larsen, as posted by Coleman. Larsen holds almost 17% of all the XRP in circulation (and probably much more). Brad Garlinghouse reportedly owns another 6.3% of all the tokens in circulation. Another XRP whale is Jed McCaleb, who holds somewhere between 10% and 15% of all the tokens in circulation. Then there are a few more promoters, who altogether account for the majority of all the XRP in circulation.