I’m running a reverse Bowden setup (direct drive but filament constrained to a Bowden tube) on Klipper but here’s some things I’ve encountered.

1. Add a little padding to the runout distance (e.g. if it’s set to trigger at 7mm change it to 10). Especially in a Bowden/push config

2. If that doesn’t help check that you have your retractions dialed in. If they’re too large then you may get a scenario where it retraces back, the sensor rotates but since it’s less than the configured detection distance it doesn’t register movement. On subsequent extrusion there’s movement again and after the retraction it takes a bit to un-retract. So you get a scenario where it pulls back 4 and pushes 4 and that’s a “net 0” but it registers that it moved 8 without a detection. Having a higher detection distance helps since it will recognize movement before it hits that limit.

3. Make sure there’s no filament dust jammed in the sensor. Although but should be less prone to affect this one since it picks up on the rotation of a wheel rather than the filament directly.