I have heard that it does this to burn off extra fuel in between shifts here
...and a reflash could help. I have the same problem and I have a APS bov...a hybrid valve that recircs and VTA. One thing I notice is when the boost is low enough to recirc and I shift I do get the RPM spike. When I get enough boost that the bov will VTA the car will want to after fire instead of RPM spike.
edit: maybe not with a reflash...I think I read that wrong.