What JB4 version and what software revs are you running? What are your settings?
Post a log and an image of your user adjustable settings. Have you run map 5 and do you get the same results.
It sounds like you are referring to what to me sounds like retarded timing during a shift...sort of like a NLS (No Lift Shift), for me this was very noticeable when I was running restricted boost levels in 1st and 2nd. Pretty sure it was also the case in map 2 and know it was it map 6 but at the time I didn't put it together and haven't revisited it as map 2 ran like crap for me at the time and there is no reason for me to run it. I'll probably dial map 6 in later but for now...map 5.
2008 E88--2 years on 100% E85. Too much to list..
2008 E60--JB4/MHD--FBO and under development
2011 E90--Fuel-It! Stage 2 LPFP + TBI--Pure Stage 2 Turbo--JB4/Flash--VRSF 7" FMIC--DP 538/581
2013 Mini JCW--Tune--DP--FMIC--a couple Fuel-It! goodies