Some skills had some clumsy coding where they would apply different AF's during an ongoing AF. When that occurred, and the secondary AF wore off, you'd still get the echo of the primary AF being dropped.

Which is what confused you.

I did some tinkering so you should get different echoes for each.

You'll notice in combat you got an echo. That echo indicated the start of a new SUB-bonus of the spell. The subsequent echo was it wearing off. The later echo was the actual skill wearing off.