I have had this problem in the past with Mojo Mail and IKonboard. Both change the owner of the file so it does not match the customer account. I had to change it from command line.
Can't change file permissions using theme: cPanel X v2.2.5. I'm able to change permissions (CHMOD) using ftp client. Just cant do it from cPanel and file manager.
The ones I editted did not have the space. Again, I'm not sure if this was CPanel's X theme or a custom X theme. All of ours are fixed now, so I don't have anything to compare it to.