darrenj...
Are the bags end-to-end, or side-to-side?
If side-to-side then, even if they are butted up to each other (but not too tightly), a Banner Laser-Ranging-Eye should be able to easily discern the passing of a bag.
If end-to-end... that might be more problematic.
Also... you might consider a "voting-pair", each from different points of view. If both agree that a bag has passed then you can believe it.
Or, maybe... you are counting in the wrong place... How about counting the bags, up line, as they are filled, or tied?
What is the orientation of the bags?
Can you count in a more appropriate place?