Custom PHP Application in subdirectory of WordPress not working

[bkennedy]

I have a PHP application that was working perfectly in a subdirectory of my site. Then I moved WordPress into the root directory, so my app is basically in a subdirectory of WP. Once I figured out some session file problems, I had it mostly working except for this bit. The app has its own htaccess file, and I'm sure that's the problem. I use mod_rewrite for a lot of things in the app. The problem occurs with these rules in the app's .htaccess...

RewriteRule ^simple([/]*\S)?$ view_simple.php$1 [L]
RewriteRule ^simple/(\S)?$ view_simple.php$1 [L]

Going to www.example.com/appfolder/simple works fine, but when I try going to www.example.com/appfolder/simple/?variable=value I get a WordPress 404 error, rather than view_simple.php utilizing variable=value like it should

Like I said, it worked before I put WordPress in the root directory. Nothing in the appfolder changed.

Here's the pertinent part of the directory structure...
example.com
---.htaccess
---wp-admin
---wp-content
---wp-includes
---appfolder
------.htaccess
------view_simple.php

Any ideas on why this would happen? Is this the right place to post this question? An help is appreciated, as this is currently on a production website.

Thanks in advance!
Bob

[bkennedy]

I really don't want to resort to using the actual filenames, but I can if I have to. If I go to the url, but use the full filename (view_simple.php?variable=value) it works fine.
Can you help me avoid that fate?