this is a little moldy, but I have to add a me too to share; you aren't alone. I've been chasing this for a week and finally gave up on 6006 and went back to the old OS... problem GONE. No matter what I did, the base tune would be wonderful and the tunes in folders 1,2,3, and 4 would defuel terribly. If I ran the tune as a single 6006 it was fine; put it in dsp5 and again nothing shifted well but the base tune.
The difference here though, is that I can't truly blame the OS! I re-wrote the tunes in the old OS converted to dsp5 (02444105) and every tune except tune 3 (dsp folder 2) was perfect. I copied all folders from dsp folder 1 into dsp folder 2 and it still had the bad de-fuel! WTF? So, I gave up. I went into tune 5 and added a little timing, reflashed and took the truck out -- all good. For the hell of it, I slipped it into dsp tune 3 and lo and behold the mystery defueling was gone. I am just totally puzzled!
I decided to just tell my buddy (I'm tuning his truck) to drive it this way for a while and see if 3 keeps working or gets screwy again. I'm tempted on one hand to tune that folder back to the level it was, but on the other hand I finally have 4 out of 5 tunes working and would hate to lose that, lol. I am at my whit's end with this "ghost".