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 AW E88 Auto running on 100% E85
BMS CP, DCIs, & OCC--
E85 CP injection, and Fuel-It! Stage 3 LPFP--
M3 FSB, RCAs, & FCAs--
Whiteline RSFBs, and DBs--
ER SS brakelines--
Stoptech slotted rotors w/Ferodo pads--
Apex Arc 8s w/Nitto NT05's--
Wavetrac LSD & Ohlins R & T Waiting on install:
Nothing...give it a few