Maybe the user who runs the Apache is not the owner (or doesn't belong to the right group) and this is why you get the issues. What's clear is that files should not have 0777 permissions as this is a security hole. Can you ask to your hosting provider about this?
Does "Repair" set all permission to 644? What is doing the Repair button exactly?
Yes, the "repair" option set file permissions to 644 and directory permissions to 755.
Last edit: 3 months 3 weeks ago by Jose. Reason: Add more info
Thank you very much. I talked to my hoster and it was theil mistake as they upgraded Joomla. The have corrected the permissions and now FileManager is happy with that.