I am having this same issue both with an install of mint and fever. I recently migrated my site to a new web host and the site itself is working fine, however, when I attempt to navigate to one of the third party applications via http://mydomain.com/app I am unable to get the application to load. Actually, in one instance (mint) the page loads but does not apply any formatting, in the other instance (fever) I get a 404.
I attempted your suggestions, for fever I navigated to http://mydomain.com/fever/boot.php but to no avail.
Just to let you know I have my wordpress install in a wordpress folder in my root directory. This is the same directory in which my mint and fever folders reside. I have copied the exact same structure and databases from my previous server. I have also copied the same .htaccess file into my server’s root directory.
Thank you in advance for any help.