Assuming your BCS and BCA are working properly, these are now your possibilities:
1. Vacuum leak somewhere. Use carb cleaner at idle, and spray it on each device and vacuum connection carefully. Your idle will change when you found your leak, as the manifold vacuum will suck the carb cleaner in and combust it. Pay particular attention to the T fitting under the nosedrive of the supercharger, and BE CAREFUL.
2. LIM/SC gasket leak.
3. Bad MAP sensor causing an inaccurate reading.
4. PCM is dumping or limiting boost for some reason. Block all 4 tires and set the parking brake. Put a TRUSTED companion in the car and have them firmly hold the brake in DRIVE while running the engine RPM'* up to 4000 or so. Stand by the FENDER and watch the actuator with your head out of the way of the hood if the car moves (don't do this in front of the garage door). Does it still go full travel on the actuator?