I have a site set up with drupal, everything going fine. I then added a subdomain, and that too was fine until I went to enable a custom theme that was under the sites/all/themes folder. The theme does not show properly in the admin panel (no thumbnail), and when activated, the site appears to have no structure at all.
The theme I am trying to use works flawlessly on my other sites, so the theme itself is not a problem. I noticed the same happens with modules under that all/ folder. It is able to use anything under the root themes and modules folder however.
So something is preventing it from properly loading/reading the sites/all/ folder. Dumping everything into the core folder is not ideal of course, but I can't figure out the problem.
Edit: RESOLVED! Somehow an htaccess file got into the sites folder with a redirect in it. Causing just the subdomain to not see the subfolders properly, only root.