Well something was DEFFINETLY wrong with that second car. Mismatched parts or something. There is no way that a properly tuned car with aftermarket aluminum heads and headers will dyno less than a stock iron head'd motor with exhaust manifolds, even with a port job. My guess is either his tune was way off, his cam was not matched up correctly for his car or a mixture of all the above.
I used to run a '95 Trans Am and had moderate mods done and had a buddy with a '96 and more money than brains. This was back in the late 90's and LT1 parts were still being developed and everytime a new part came out he HAD to have it. Well the problem was even though he had twice the parts I did he could never touch me at the track. He used to get so frustrated with it till one day my car was at teh shop getting a 383 kit installed and he talked to the owner of the shop about his car and the guy told him. He had a bunch of nice parts but nothing worked with one another and he ended up having his motor tore down and rebuilt using different heads, cam and LT4 intake and the damn thing came to life. Needless to say I couldnt touch him after that.........till I got my bottle