Chances are that your PHP script is generating references to CSS and/or images with relative paths, such as:
Since your page is now appearing to the browser in a subdirectory, this ends up getting interpreted as the image being loaded from:
Since that doesn't exist, the image cannot be loaded.
RewriteBase won't help you here. You will need to update your application such that it generates absolute paths for images, e.g:
(The leading slash is the critical change here.)