Picture is a better representation of what problem I'm having. Comparator does not output a signal from the stacked hopper while items are travelling through unless a redstone signal is active near it but not powering the hopper.

The left side has no output from the comparator while the items are moving. The right side does receive output because of an indirect redstone signal. This make no sense - almost as if the redstone is slowing the item down enough for the comparator to make a signal. Note that the redstone signal does not close the hopper.