I don't get the clunking you describe.
The up changes in my box were becoming jerky and I never saw it as a problem but when I pulled to a stop the engine would dip below tickover before the clutch released.
They updated the software and that solved the clutch releasing late problem.
The jerky change problem was caused by the clutch actuator being poorly adjusted to start with then there was a fair amount of air in the hydraulic clutch line.
The clutch fluid was bled of air and the actuator adjusted. The changes are now smoother but at the same time faster. I'm not sure if the faster change is due to the new software though.
I wonder if your clutch actuator is poorly adjusted and not letting the clutch release fully causing the gears to crunch when selected?