It looks like that the issue occurs when items are 'nudged' in order to fit an item being sideloaded.
Setup:
- The two wired belt segments in the screenshots are wired to "Read belt contents; pulse".
- The adjacent combinators are simple counters (Input: Gears * K > Output: Gear, wired to themselves).
- The lights show the current value of each counter.
- "K" comes from the constant combinator; enabling this combinator serves to start the test case. Disabling it resets everything
- The upper belt/light/combinator section works as expected and counts 5 gears all the time.
- The lower belt/light/combinator section consistently counts 4 gears in this particular case.
- "Creative Mode", used solely for the purpose of building this as an isolated test case (namely the power source)
- "Picker Extended" was also enabled, but should not be required.
- If all of the gears are on the top lane of the belt, the issue does not occur. Likewise, if all the gears are on the bottom lane of the belt, the issue does not occur.
- That said, I don't think the mix of the belt lanes itself is the issue. The save that inspired me to condense this down to a simple test case had a single lane being input from two different directions at once. (The original goal was a belt-based alternator that'd force a 50/50 split of items)
- BenjaminK on IRC says the he's "never made a bug report, and i feel like i made a contribution!", so here's a cursory mention by his request. (To be fair, the lights were his idea...)