WordPress Mod Rewrite Make Subdirectory 404 Error

Last night, I getting lots of 404 error while using Google to search my own blog index page, I realized there is something wrong about my blog.

My user-created-outside-of-WP folder is throwing a 404 when trying to access it. Now for some details:

Blog www.moon-blog.com : normal WP blog. Permalinks "/%year%/%monthnum%/%postname%.html" through mod_rewrite in the default .htaccess file WP created.

Subdirectory www.moon-blog.com/MySubdirectory/): normal PHP application. User defind permalinks. Located at directory "/MySubdirectory/".

The problem is that the WordPress thinks My Subdirectory is 404, and do not allow Google to index my files.

I Try add some of php code into my php application to resolve this problem:

header("Status: 200 OK");

After adding that code, my PHP application in the subdirectory do not return 404 error again.