Oh boy, I am so sorry @@raynebc and anybody who read this. I figured out the problem. It is not a Toolkit problem and it is not an EoF problem it is a Berneer problem... After re-looking at the above GIF, I noticed a peculiar thing, "Why is there a 5 fret width on the first 3 notes?" Looking via EoF I noticed that the FHP was 1ms too late, and Rocksmith didn't know what to make a of handshape beginning one instant and FHP changing 1ms later. On Oct 8, I was making tiny resync tweaks in the intro and despite anchors in place, EoF export recalculations must have shifted something by 1ms due to round off or something, without me noticing, and screwed up the FHP, which interestingly, only removed the lane highlights.... Man, testing and re-testing and re-re-testing a custom before release is so important.
raynebc, I simply made a handshape marking for both series of 3 notes to show that each set of 3 notes could be nicely played with one handshape, which by defintion should highlight the left and right lane with blue highlights. Am I misunderstanding your question?
Berneer's post in Non-Appearing Handshape Lane Highlight issue was marked as the answer