CSS files being read from the wrong path

I have a site at https://www.mydomain.com/ and a staging site at https://www.mydomain.com/staging/. On the staging site I’ve updated FVM from 2.8.8 to 3.03. Without CSS processing the link to the theme style.css in the html of a page is
href=’https://www.mydomain.com/staging/files/themes/christchurch/style.css?ver=7′
(wp-content is a non-standard location).
With CSS processing enabled (merging files, with or without minimisation) the data copied into the merged file comes from a file on a different path: https://www.mydomain.com/files/themes/christchurch/style.css. That is, it is reading the file from the live site, not the staging site. The other CSS files are the same on the live site and the staging site so I can’t tell which are being read.

After updating FVM to 3.04 this problem is still present but 2 of the 5 css files which were previously merged are now left out. There seems to be something screwed up with the merging.