I've just received a follow up e-mail from Logitech.
They have closed my support case, and "Escalated" it to their development team in order to get a fix.
Temporary solution? Uninstall SetPoint. Unfortunately, this means you don't get to use any of the additional programmable buttons. However, I have found a way round the problem - simply edit the XML configuration directly - it seems they load it happily, but don't save it. Nice.
I'm not holding my breath for a patch anytime soon!