FWIW, I experienced a similar phenomenum with an LS1 motor and porting the intake. I actually dynoed the two back to back (stock LS6 vs. ported LS6 intake) and lost power on the ported intake...the reason is that even though airflow was increased my runner speed was diminished and this apparently was a stronger effect than the increased airflow.
The porting consisted of opening up runners slightly, open up throttle inlet slightly, and smoothing all the runners.
copy and paste this link if you want to see, its the third graph down. We did three pulls with each intake and the results showed the same loss of power on each pull.
http://www24.brinkster.com/ezerner/b1camdyno.htm (copy and paste to browser, direct clicking doesnt usually work)
