So, finally, I'm on day 3 of a stable configuration. In desperation I changed the firmware of my wireless access point to one of the alternatives - specifically DD-WRT. So the problem looks like a conflict between the firmware of the Pronto and the firmware of the WAP54G. The problems all started when I installed the Dec 09 firmware on the Pronto which was the firmware that started supporting WPA, so it wouldn't surprise me if the incompatibility came in with that change.

Since flashing the access point to DD-WRT I've had no command failed errors - in fact last night I updated the wireless network to start using WPA encryption again without any problems.

It is supremely annoying that a device as expensive as this should only be compatible with certain wireless access points, and it should probably be noted that the WAP54G isn't one of them.

Thanks to everyone who helped out.