I would highly doubt it is actually compressor surge (especially not with turbos that size) its likely the tune. Some Tuners like to pull back a ton of timing (which essentially causes a misfire) to make a car spool faster on the dyno, if this practice is used anywhere other than the dyno it makes the car stutter between shifts. Also a similar thing can happen if the transient throttle isn't tuned correctly, an severely rich condition can cause a misfire. I would take up those issues with the tuner.