Unfortunately, I haven't seen Stigmata
, so I can't comment on the validity of what the film said about the Gospel of Thomas. I can tell you, however, a bit about what we know about it:
The gospel was discovered in Egypt 1948, and is believed to have been written at the beginning of the 3rd century AD. The text itself is a collection of sayings of Jesus which follow no particular order and contain no biographical narriative. Nothing is mentioned about Jesus' death or resurrection.
What scripture scholars have found facinating about this gospel is that there are significant paralells between the sayings of Jesus in Thomas and in the Synoptic Gospels. Some have gone as far as to say the Gospel of Thomas is the basis for an unknown collection of sayings called "Q" which is believed to be one of the sources of Matthew's and Luke's gospel, however this theory is not widely accepted.
The reason the Gospel of Thomas has not had acceptance is because some of the other sayings reflect elements of an early Christian movement called Gnosticism, which was condemned as herasy by the Council of Nicea in 325 AD. In a nutshell, Gnosticism teaches Jesus' humanity was only incidental to our salvation meaning Jesus' revelation alone of true knowledge of the world around us is the only thing that saves people (which is counter to Chruch teaching that Jesus was both human and divine: if Jesus were not human, he could not have been put to death; his crucifixion and resurrection are what saves us), the soul's dependence on the body is conemned, and strangely, female must be "made male" in order to enter heaven.
I hope I haven't gotten too arcane here. Most scripture scholarship as little more than an educated guess, but I hope I have shed some light on Thomas, and why it is not recognized.
BTW, Cflak, the only part of your answer I take issue with is the part where the Jesuits have a very large role in Catholic doctrine (at least nowdays).