If you read the actual paper referenced [0] you'll see that they explicitly mention this. Since they assumed that users were interactively trying to change their foot print, the looked at uses who had changed their settings within 1-2 hours:
"We ran our algorithm over the set of users whose cookies indicated that they were returning to the site 1-2 hours or more after their first visit, and who now had a different fingerprint. Excluding users whose fingerprints changed because they disabled javascript (a common case in response to visiting panopticlick.eff.org, but perhaps not so common in the real world), our heuristic made a correct guess in 65% of cases, an incorrect guess in 0.56% of cases, and no guess in 35% of cases. 99.1% of guesses were correct, while the false positive rate was 0.86%. Our algorithm was clearly very crude, and no doubt could be significantly improved with effort." (any typos here are likely the result of copy/pasting from the pdf)