I worked with Jerry Magnuson and TRD on a "bypass problem" with Eaton supercharger kits (back in 1997-98). I found the transition from "spinning blower in vacuum" to "throttle open" would buck and/or stumble the application of throttle. Jerry's system had a vacuum line controlling the bypass valve, and by installing an .022" restriction in the vacuum line, the "reboost" was ramped in over about 800 milliseconds, which the ECU could handle easily.
When the blower is spinning, and you close the throttle, it acts as a "booster" vacuum pump in addition to the engine capacity. Reopening the throttle can drive the measured airflow beyond the capability of the ECU (momentarily.) Using a portable oscilloscope, I was seeing a 5 volt circuit exceed 5.24 volts (where 4.9 volt was the maximum useable signal in the software).
It all reminds me of the "method" needed to test supersonic airplane design. It is impossible to blow air supersonic with a fan, but if you put a big enough vaccum tank behind it, atmospheric air will easily go supersonic into that big "hole". A blower in front of a vacuum pump, becomes part of the vacuum tank when you come off the throttle. Crazy stuff happens when you reopen that throttle.
If yours has that small vacuum line controlling the bypass, you might try a .023" wire welder tip to see if it helps your throttle control. I don't actually know what your control system is, of course, but thought I could share my ancient history "memory". We wound up installing that little restrictor in thousands of kits and ended the complaints.