Any puzzles that looked completed but have a different solution to count towards final count?

I've completed most of the game and am currently stuck on The Challenge. Only gotten as far as completing the invisible maze and can't seem to get enough time to figure out the columns.

Using this list (more spoilers)...

https://www.reddit.com/r/TheWitness/comments/465cku/spoilers_list_of_all_puzzles/

I've figured out I should have a total of 517 puzzles completed, and the only ones I'm missing are...

509.First pillar puzzle 510.Second pillar puzzle 511.Rewarded for completing the challenge (timer puzzle?) 512.Rewarded with previous (timer puzzle?) 513.Rewarded with previous (timer puzzle?) 521.Movie puzzle 4 (solution located in mausoleum opened by completing the challenge)

However my save listing shows only 515 puzzles completed. I've reviewed the whole island and each puzzle twice and can't figure out what I'm missing. Do certain puzzles in The Challenge not count until you 100% complete The Challenge? Does the elevator only count while you're flying with it as it's resetting the game? Are there some puzzles that look completed but don't count towards the final count unless you complete them in some specific way?

Thanks!