Does an exchange of only virtual currencies fall under FinCEN regulations? If a business only exchanges between say bitcoin, litecoin and namecoin. No fiat currencies. Does it still fall under finCEN's regulations?
Your guess is as good as anybody else's.   FinCEN's guidelines read:


  The term "money transmission services" means "the acceptance of currency, funds, or other value that substitutes for currency from one person and the transmission of currency, funds, or other value that substitutes for currency to another location or person by any means."


That's as broad as you can get.  Bottles of Tide detergent apparently serve as a form of value that substitutes for currency, so going by that FinCEN could go after your corner market for not registering as a money transmitter for delivering tide to your door without verifying that you were the person who paid for the order (and keeping records for five years, and ... etc., etc., etc.).  Now I know they probably wouldn't stoop to doing that ... just like how the IRS wouldn't treat non-profits differently based on the political aims of the non-profit.  

That's called totalitarianism.  The laws get interpreted such that the government gets total control over everyone and everything.