Further further experimenting... it appears another hopper beneath a hopper is pulling the item so fast it's not causing an update to the comparator.
"Quick hopper behavior" is a more proper title
A quick patch to the unloader design, have 1 hopper unload into a chest before another hopper... This will cause the minecart to stop and unload.
After further experimenting it looks like its not a minecart issue but a hopper/comparator issue. It's now an issue in both singleplayer/multiplayer. 1 item passing through a hopper at a time (like how a minecart hopper drops items into the hopper) does not cause the comparator to update and output a signal at all.
[media]Confirmed
Can confirm. Very annoying bug indeed.
This is definitely not resolved.