What I did:
I placed a hopper so it outputs to a chest, then connected a comparator so that its input was that hopper. I tossed in one rotten flesh. Waited for it to pass through to the chest. Then opened the hopper inventory and placed one rotten flesh.

What I expected:
I expected each action (tossing one flesh into the hopper, and placing one rotten flesh into the inventory) to activate the comparator on its way through.

What I found:
Placing things one at a time into the hopper inventory will never activate the comparator, while tossing them in one at a time always does.

It's worked that way since 1.5.1.