Right, well I seem to have fixed it, with a workaround.
Untick "Use Socket For PHP-FPM" in ALL the sites, even the working ones.
Then service php5-fpm restart.
That's got me working - but I have a feeling this isn't ideal, as many guides say socket is preferable.
So many unanswered questions here, but I'm 4 unpaid days behind now, so it can wait until I've caught up, but I'd love to get to reason behind this one day.