Look at if the ECU is Delphi, if so, it is probation that it is the cause of the problem, anyway there are a series of procedures that are carried out with the original Scaner or the Superscan of Dec Automotive that make the memorization of the parameters for the butterfly body.
Try also memorize the motorized cripose by putting the contact for 40 segs. Without doing anything else, if the air filter is not placed, noise is heard in the body, it means that you are looking for the stops to memorize them, you remove the contact you wait a few seconds and that's it.
If the problem is memorization, it is possible that it has been corrected; If not KAPUT control unit except a bad mass or connection in electrical connections. Care with the connections of the main battery terminals.
Good luck and greetings.