On the attached PDFs you will notice that if you use the text extractor to get the text locations - text on the top of the page has a higher y coordinate than text on the lower part of the page. So if you use the text x/y cord to place a highlight, the y coordinate ends up being on the opposite half of the page.
Attached, bad-highlighted.pdf shows where the highlights are being placed. The coordinates for the highlights are the locations recieved from the location of the words "Engine coolant" and "Battery:"
Attached, bad.pdf - this is the orginal pdf prior to placeing highlights