yeah I know, but passing the css file in the header through that seemed to be the root of the issue. It didn't seem to like the addition of the variable ver to the end. Hence why I thought that was the issue.
strange that it only seems to be happening for multi site, it appears that going through the ms-files.php script causes the mime type to not be recognised. possibly because it isn't expecting a variable at the end?
It's actually the /files/ in the path to the CSS file. In single WP you don't have that rewrite rule. If you change the folder name to something else and update the enqueue_style call, you should be fine.