It's been shown over and over that the TRE slows most Hayabusas in the qtr. Brock Davidson has been proving that forever. Just like Greg said, it's because of the fueling and ram-aor compensation of the 5th gear map.
I tested the old school Ivan TRE from repeatable 1st gear to 4th gear and 2nd gear to 5th gear roll-on tests. With the TRE, the initial acceleration was better with the TRE but once I made the next gear change the bike lost acceleration substanially through out the next gears. I personally saw a little more than a .10 et and almost 2mph in the qtr. 60ft was slightly better with the TRE but lost a bunch from there on.
Now that I have been using Greg's reflasher, I have an opportunity to play around with the timing throughout the whole RPM spectrum. Kick ass!!