I don't quite remember how I got to that stage, I'm afraid - but I'll do my best to tell you what I do remember.
I had a long vocals region on a track that had been recorded at a tempo of around 100bpm. But I later wanted to adjust the track speed to 120bpm and so I tried adjusting the vocals-region as a whole to 120bpm by first turning on Flex & Follow and then changing the bpm from 100 to 120bpm in the LCD. I seem to remember that making this change to the LCD value did result in some changes to the position of the transient markers in the vocals region (but certainly didn't get them to 'line up' perfectly for the new timing). I couldn't be bothered to go in and manually adjust the start times of the vocal parts, so instead I cut out the parts of the vocals region that I wanted to use in Live Loops and pasted these in directly to the Live Loops cells for editing in the Audio Editor.
Once the regions were in Live Loops, I used the Audio Editor, making a few adjustments to the Loop Start and Cell Start as needed in the ruler area. At some point, I realized that the values showing in the Cell Inspector for some of the cells were now these SMPTE ones, not the default ones - but I've no idea if those values changed while I was in the Audio Editor or if they were already that way when I dragged the regions into Live Loops in the first place.
I hope my description might shed some light on what went wrong when!
(On the subject of making global changes using Flex, I was trying to adjust the tempo in a lazy way by changing the vocal region as a whole rather than going through section by section, but this didn't work: at the new speed the vocals were not quite in sync to the beat. Is there a lazy way to automatically adjust an entire recorded audio region so that its various elements 'fit' in the right place when played back at a new speed?)