I think this one may be resolved.
Install of version 2.1 was an in-place upgrade to a previous version 2.0, which in turn was an upgrade from version 1.
The tree at \%BOOTDISK%\users\username\appdata\local\Z-Systems contained folders for all 3 versions, each of which contained xml config files.
Uninstalling Finestra and deleting all relevant folders associated with it, rebooting and reinstalling clean seems to have cured the problem. All options are now saved as required.