Thanks for all your support!
I think that I have got my head around how it works: the global settings ALLOW a plugin to be used by pages or filters, where they can be disabled (but not enabled). Is this correct?
If so, I respectfully suggest that you change the wording on the globals settings page from:
'Select the plugins you would like to disable site wide. This will allow you to not load the plugin on any page unless it is specifically allowed in the post or page.'
to something like:
"If enabled, the following plugins may be disabled on pages or filters. The list is also the default unless altered on a page or filter"
All of this aside: I am still unable to save the default plugin order.