I have noticed this myself with one AI getting far ahead.
First time was with Persia. They were the obvious benefitor of the GPT bug (had 30K gold at one point). They also are Scientific.
In my current game (with beta patch), Greece has pulled ahead by 5+techs by the early industrial age. Hard to say how long they have had this much of a lead since they are one the other major continent in this game. When first contacted, the other civs on this continent appeared to be about even in terms of tech, resources/luxuries, cities and area size. This was early to mid-Middle Ages.
I suspect that the Science Leader (SL) is an unbalancer. Especially for Science oriented civs. What is the chance... 5% for Science trait, 1% for other civs? As I have posted previously, the SL seems to have a good chance of knocking the tech race out of balance.
I must say this about C3C though... they have greatly (at least it appears this way at this point) improved the common experience of Vanilla/PTW games were every civ instantly traded techs between themselves which made for a homogeneous game. I'm seeing much more variety in the civs now.