Sometimes, when doing this quest, usually when you have a longer string of 'pings' it will lag or something and two color pillars will 'ping' at the same time. It's impossible to know which is first without just guessing. I think maybe it's the script lagging when it's a longer memory run?
I think that's a feature of the quest to prove how difficult EFU quests are. It should stay as is, so you have to earn it.
I'd prefer the input of an actual DM but thank you for you're comment that has nothing to do with this bug report.
Haven't responded as I don't have much to offer for a fix.
I imagine it's something along what you wrote, but the script is pretty minimal so maybe other processes might slow it down and there's more chance it will show in longer runs. Unfortunate it happens, but as there's no risk involved (a useless trivia detail is that in the original design there was risk involved!), it will probably stay as is. Take it as an opportunity to guess :)
FWIW I don't think Damien meant anything bad there, and I'm quite liking what he wrote. Maybe the interval should be randomized somewhat to also have shorter intervals between pings to make the quest a tiny bit harder. Something for the future, perhaps!