SOLVED
I’m not much of a developer but I managed to trace the problem variable back to wp-config and the line …
define( 'WPCACHEHOME', '/home/sites/[MYDOMAIN]/public_html/wp-content/plugins/wp-super-cache/' ); //Added by WP-Cache Manager
as the source of the old URL.
I assume on install wp super cache is only checking that line exists rather than is correct for the current site location. I’m not sure if it’s feasible, maybe there’s a reason you don;t do that, but it would be better if it could.
Thanks for a great plugin anyway.