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Well my teenage self would know this much better having messed around with the 1541 drives. I never used the more advanced drive mentioned here. My theory is that the clock was a badly written app that used an NMI to draw itself on the screen. This would interfere with the drive timing in a consistent fashion, based on the size of the clock. It would almost act as encryption. So a file written with a particular size of the clock would cause a pattern of rotational delay that needed to be matched every time it was read in the future. You could even set up varying permissions on different files with the clock being a specific size when you wrote each of them. The user could have noted that it worked only when they had the clock up without understanding why it was necessary. Make sense?