Found this on the net. If true, then Ford wasn't willing to pay the price asked by whoever owns the GT40 name. I guess Ford wasn't smart enough to license the name when it was first produced.
To quote the Motor Magazine, February 2002, page 12.
"But the new GT40 is bigger and longer than it's namesake (which stood just 40 inches tall) and is seen by Mays' as Ford's 'supercar'. The remake stands four inches taller and was almost named the GT44 until Ford was able to buy back the rights to the GT40 name from the American Saffir company, which had been licenced to produce parts for the GT40."