Hi
Typically, September is wetter in and around Pokhara and gets less sunshine. In the last couple of years (at least) the monsoon has finished later and September has received more rain (and more constant rain in KTM in 2010 at least).
Sticking my neck out, I'd suggest early monsoon remains more predictable with the rain patterns as described by destinantionnp.
Having said this, whatever rain falls, the ABC trek gets the ful force of it while much of the Annapurna Circuit is in the rain shadow area and is relatively dry.
scoodly