Wasn't there a post, somewhere around here, that KG was inserting two "text" Guide items, and that popping the OPF open and removing the second reference solved the issue? And not using "Start" other than as the title? I know that KG has, on a number of occasions, produced two "start" (text) locations for us via Previewer. This seems to resolve when the book is uploaded to KDP.
However, if you actually removed all anchors, etc., and simply set the start point to a specific file, i.e., html/content, then that start location should absolutely start there, and nowhere else.
Did you check (no offense) to ensure that the KG portion of your INDD plug-in did NOT set a different "start" location with the "text" TYPE in the Guide? Which would override any "start" locations you have set, to the best of my knowledge?