uploads to folder outside drupal root

Issue Summary

I have an interesting issue. I have a configuration that involves a drupal installation called /drupal in my public_html directory, and some rewrite rules in my htaccess file so that when someone goes to the domain of my site, they get the content from the /drupal directory. This works great in every respect except in one instance - when I upload a file, a new sites directory is created at the root level of my server instead of just uploading the file to the respective sites folder in the drupal installation. So I essentially have this:

public_html/drupal/sites/default/files/...
public_html/sites/default/files/...

When I browse for files (using IMCE), oddly enough, I am able to browse for the files in public_html/drupal/sites/default/files.

Is there something I can change in the code that would correct for this sort of installation?

Thanks in advance!