I think the example works more quickly than it should due to the line "if(ff.clock>1) ff.clock=1;" Every time the clock goes over 1, wouldn't you mod the clock value, not set it to 1 exactly?
So what this line does (which is in the section of code where a flash alters the fireflies around it) is that after advancing the other fireflies clocks, if any are over 1 then it puts them in the right state to flash on the next time they're evaluated. If you mod it, then you would have the logic:
"if I'm a firefly and see my neighbour flash while just about to flashing myself, don't flash but reset my clock to part way through the cycle"
rather than
"if I'm a firefly and see my neighbour flash while just about to flashing myself, flash as well"
Edit - setting it to one ensures that each neighbour can't keep adding to the clock, advancing it to a random point in the cycle.
It does make (intuitive) sense, though, because the only time that makes a significant difference is when a lot of fireflies flash around one firefly simultaneously, in which case the firefly wouldn't decide to flash twice in a row but instead interpret it as a singular flash. And if a firefly sees another one flash when it's about to, it would naturally want to synchronize its flashing with the other.