Interesting tool.
It needs a couple of options.
One button option should indicative the person is unable to see any difference, and move on, a second button option should be the box they indicated they were sure is a different colour was not right, and move on. Additionally the tool should map the position of the box when they were sure but were wrong, and keep a record as the person works though the game, just in case their screen is not perfect. Perhaps even come back to the same colour scheme but put the different colour in a different part of the screen.
It shouldn't be forgotten that people actually tune into slightly different colours given some time - fruit and vegetable graders who visually inspect, and those who are working hard to purchase the just right fruit and vegs, find given time and practice, they'll slowly learn to perceive the very minor differences in certain shades or hues.
Edit twice, a couple mins later and another couple for additional clarification.
I think the screen can definitely be a factor. I'm using a monitor with a TN type panel, and the viewing angle will change the amount of contrast which makes a difference in the later stages. Some would have been impossible to pass first time without shifting my head, even if my eyes are up to the task.
Thanks for the feedback! My initial idea was to make something super simple for children, this is why I didn't add any buttons (there are 0 buttons in any of my games on my website, except for "start" button). But let me see if there are any alternative solution.