After a bit of amateur internet sleuthing I have pieced together my theory.
I can find no substantiation to the claim that this plane flew between the U.S. and MUGM (Guantanamo Bay Airport). The website
http://flightaware.com does not appear to list any such flights all the way back to the beginning of 2005 according to my friend who is a pilot and has a subscription to the service.
The manager of the aircraft during the time of the alleged flights to MUGM was
http://www.arijets.com/ Air Rutter. They are a well known, reputable, and established air charter company. Definitely NOT a CIA front company. They have no record of the plane being flown to Guantanamo.
The plane was then sold to two Brazillians on August 30th of this year and the Brazillian men claim they sold it to two Florida men on September 16th.
The two Brazillian men own the company Donna Blue which does not appear to actually exist and could easily be a CIA front company. Though it is not a very cleverly concealed front company nor would it stand up to even cursory investigation but if the way the CIA handled Valerie Plames all important covert status is to be held as an example then yeah....it could be.
I find it more likely, however, to be a drug smuggling enterprise in which the actors thought to disguise their dealings with charter flights around the Caribbean and a not so well put together front company to register the plane legitimately. Being drug dealers and having a goal of flying several tons of narcotics hither and yon they cannot hire the most reputable pilots out there so they hire a bum and he crashes the plane full of narco in the middle of Mexico.
If the CIA story is to be believed then we must believe that they were so very clever as to hide the flight data of flights to gitmo which takes some bit of effort to come by anyway but forgot to put together a decent front company to hide their activities. Maybe the guy in charge of that was in the john helping himself to some of the product....
We all love to find the super sekrut spy game stuff but sometimes a cigar is just a cigar.
