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--Fuel-It! Stage 4 LPFP & PI--PS2 turbos--JB4/MHD--FBO--662whp/604wtq
2011 E90--Fuel-It! S2BL LPFP and PI--PS2 Turbo--JB4/MHD--FBO--546whp/589wtq
2013 Mini JCW--Tune--DP--FMIC--a couple Fuel-It! goodies--265whp/320wtq
2015 F82--Fuel-It! Stage 3 LPFP & PI--PS2 Turbos-- JB4/BM3-FBO