With a rebuilt turbo it should be more efficent, meaning more airflow at the same psi of restriction. So actually if it was tuned on map it would be more likely to ping and if on maf same thing but max it out sooner and go into rich mapping to avoid detonation, maybe thats why.
A new turbo wont give you more boost on the same setting, (i dont care who you are) its just a setting to tell the wastegate when to open.
My 2 cents.