It shouldn't matter in newer systems that could just use image analysis I'd imagine, but a lot of school systems don't exactly have the newest technology. I dunno about where you are, but out here, whenever I was in school and we would take a machine-scored test, they'd always ask, "so, does everyone have a #2 pencil?"
anyway, you could ask a teacher to perhaps look at your sheet + the scoring for the first section to see if there are discrepancies, if you're interested.