Hoppers stop processing items at a certain point when unpowered shortly, causing the items to build up.
Notice that this does not happen initially, but only after you relog or reload the chunks. (Same as MC-74729 which was fixed in 1.8)
This bug occurs up till an off-signal of 3 ticks. Which incidentally is (almost) equal to the speed hoppers process items.

Update: Whilst trying to work around this bug, I discovered more nonsense. I could create a seperate Issue altogether, but I believe the two are related and it might help fixing the Bug.
I tried to let the hoppers process 2 items at a time instead of one, but the result was just as irregular.
This time the items will arrange in a specific, but non linear pattern. (see "update" screenshot). This behaviour occurs with several different pulse lengths

Could also be related to MC-11193