Hey David,
Thanks for looking at this.
The file I was doing the demo in is one of my sketchpads and I have been known to use every bar available at times... (somewhere around 17500 bars I think?) Probably dabbling in alchemy but never an issue actually. Except if I get buggy with time signatures and stuff I have seen material turn grey at the end of one of these 9 hour files. Otherwise long files have never seemed to be a problem, which is a tremendous feat for LOGIC IMHO. I work in more normal length files when focusing on a project.
THE GOOD NEWS IS
I can report that I have been able to stop the odd behavior by turning off everything in the chase tab.
I haven't taken the time to figure out which of those ticked boxes was the culprit, but it seems the problem was in that set of preferences.
I'd prefer to use the chase feature on occasion if I choose to... but for now I just turned it all off.
Thought I'd answer your questions anyway just for the record...
Project sync is the same.
The start marker is at zero