I will check the grounds. I only know of the ground at the battery? If there are more, let me know. I am leaving on a 4700 mile trip out west 6-23-16.
I rode home last night and messed around. It's right at 3k. It did it before and after the flash. It's one of the reasons I bought the flash. The lower the gear, the worse it is.
Any gear, worse in lower gears, most prominent in 2nd and 3rd. A big snap in 1st will make it wheely, heh heh. That's a bit much for the old girl thought.
Scenario
70F ambient
Completely off throttle to partially open throttle (NOT a snap to full accel)
Huge difference in various rpm, 4k is OK, 2.5k is OK
Sure seems like mapping. It's partially caused by the shaft drive, you're loading one side of the gears on decel, then slapping over to the other side as you roll on and take up the driveline slack. But at 3k, it's worse as it goes from low something to way more something (fuel, I assume).
Yeah, I know what you are feeling... it's not mapping though I understand why you would think so, if I didn't know better I would too. I worked all that hard during building the maps, and going from closed throttle to open throttle can be a problem like you're experiencing, so I worked hard to smooth that transition because I ride like that too.
Now back to the battery issue - If I hadn't ridden on it, I would have a real hard time understanding it, but yeah, it showed itself as really bad upshifts. Everything else felt normal til the shift...WOW that was bad. worse in the low gears, but even cruising 4th gear around 3k then rolling the throttle on would give this big bang of power, like the TPS skipped over all the transition cells and went right to cells that gave a lot of fuel. Terrible. I would have been really flipped out and worried if I didn't have as much experience with the flash, but I knew it was not the flash, it was in the bike, so I went after it from that angle. Sure enough, found the ground at the battery was loose. tightened it up and the bike runs 100% perfect. Who in the world woulld think the battery connection would do that? BTW, the big clue was when the owner told me it did that before the flash, too... that really helped me be sure it was in the bike. Let's see if that's the case with yours. Check the battery first. Steve