Check to make sure you ran the boost and vac/boost lines to the correct ports on the solenoid. Also not sure if it matters but I have my extra port left uncapped. A boost controller can't affect anything up to wastegate pressure so it can't be affecting the vac to boost transition.
Also make sure that the solenoid is secured and not left flopping around as that could possible make some clacking noises. And as always check for boost leaks while you're at it.
If in doubt in dialing in the correct settings-
The Pansy Patrol » Greddy Profec B Spec-II: Tuning Tips for 3/S owners
Mike
