Ok gang, I've got a weird one (which I only just spotted whilst playing with wp-super-cache, but don't think that is the problem).
I have Litespeed webserver picking up all domains (* in the listener) not specified elsewhere and sending them to the MU installation.
So all MU sites are served by the same 2.6.5 installation. Distinct domains are created using the multi-site plugin.
Wp-super-cache is now working on all blogs on the installation EXCEPT a single domain. When I go to the cache settings page it says it doesn't have write access to the wp-content directory. I also can't upload files from the backend of that single domain (and sub-domains of it).
Note: Everything is running off the same web server, in the same MU installation and all are working except this single domain.
Any ideas?