just ran into this problem with my turbo setup...how do YOU boost reference? YOU don't. You have to send the carb off to get boost referenced..they go in and drill out the carb so it will receive signal under boost.
I have heard you can remove the powervalve and change the jetting around, but that is kind of a half a$$ sollution. Walts Hot Boat in California took care of me real well when I had this done. Getting a carb referenced is not cheap, but he gave me a real good deal through a company he works with.