You could also just ignore a/v wizard, and set the xorg.conf file manually. To do this add: AVWizardDone = 1 to /etc/pluto.conf. Then AV Wizard won't run again and won't touch your .conf file afaik.
Then in the admin web site, go to advanced, config, devices, choose core, the core/hybrid, on-screen orbiter and update the PK_Size and Screen Width / Height values to match whatever resolution you forced in.