I tried powering the “laggy” hopper through a block as suggested in https://www.youtube.com/watch?v=1rOC7H05hHw&t=10m, and this caused the other hoppers to emit 1 stack on the 3-tick pulse (and emit nothing on a 1-tick pulse). I guess it must have changed the tick order in some way, and it seems to work after reloading the world too.
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