Sorry for the late reply, the version 1.12.2 is most likely the problem.
I can't really tell what the bug is here, maybe something to do with redstone priority, redstone with different powers have different priorities (meaning the order things are activated within a single tick) that is even effected by east/west/south/north but that doesn't seem like the likely problem.
If you insist on 1.12.2, which you probably are because it's a pretty stable version for a lot servers, try building it in different orientations or different chunks because different chunks processes redstone differently. Redstone is surprisingly inconsistent but understandably so, it's hard to get a perfect set of rules that allow redstone to be consistent in single tick and orientation.
It's obvious the problem is with the redstone torch not picking up the signal fast enough, try this:
After the one tick pulse put two repeaters set to two ticks (one position up) and make the rest the same. It might be a problem with the repeater giving out a less than 3 redstone tick pulse because the initial pulse was so short and hopefully the second repeater will fix it.
If the problem persists, then maybe you do need stick with the slow and agonizing three tick repeater ;(