Well, that's extraordinary. I confirm that the mobi you sent me has the correct meta data for the start offsets. I don't know why they aren't in the samples.
Umm... I think, that in the KDP control panel, you can download a 'preview' which is the processed file, the mobi7 version. Perhaps you could try this and double-check that that's wrong too.
And then it becomes a matter of testing what does work at KDP. Perhaps a 'fixed' version of the mobi would work. You could try replacing the one you uploaded with that, and then download the processed file and the samples after it's been processed and see if that's better.