I think that's what everyone has been talking about. you need to, or have someone look at all the cells in the tuning range. you should see nice smooth increases or decreases.
For example if under no boost acceleration you see an increase of say 2-3 % then one cell or series of cells suddenly jumps or drops drastically that's what your problem is.
I had a similar problem with SDS. Since it was originally setup in okinawa (HOT) once i got to Alaska it would hardly start and run until i looked at the engine temp settings. there was an area that was way off in the lower temp area. once i fixed it it started and ran perfect. This will apply across the board in any engine variable like timing, boost, ect ect. lets set you are starting to make boost at 3500 BUT in the part of the map that adds or takes away fuel in that boost area is way off well again. here's another example. you start making boost at 3500... when you reach that certain boost timing is pulled or advanced 20 degrees well get my drift.
If you dropped the car at a competent tuner, that is familiar with the system you put in the car, they should be able to pinpoint the issue pretty quick.
Good luck