I was blaming firmware for this, but it's a cable issue: powered speakers will thump when powering off the III if the unit has an FC cable connected to the unit, but no FC on the other end. Power down the III before disconnecting your FC to avoid.
Just stumbled upon this post. Perhaps making sure the SPEAKER power is OFF (and the amps have had a chance to discharge) BEFORE turning anything that feeds the speaker on/off is the correct solution, regardless of firmware/FC connection/whatev? Your speakers will thank you for it – and you won't damage the voice coils by slamming them to their physical limits.