I'd check your wiring. When I did my top swap I purchased the swap kit that came with the MAP stuff and the BBV sol pig tail. The MAP harness was wired backwards (outer pins were swapped so instead of wiring A -> A, B -> B, and C -> C it was A -> C, B -> B, and C -> A) It caused mass confusion and I didn't notices it until I broke out the volt meter and started testing ends... Heck it was throwing a code for the gas tank... LOL But something simple like that can throw everything out of wack.
Also I have my BBV hooked to run complete off vacuum. Here is a diagram of what mine looks like. I assume you swapped a Gen V top on your L26 and not the Gen III so yours will be a bit different but around the BBV should be the same..
http://i698.photobucket.com/albums/v...220_172842.jpg
What I'm wondering is it being an 06, is it a security thing? My Intense PCM came with the VATS/Security and Crank Pos Sensor relearn procedure.