I have a file in the store root (Zen Cart is in the 'store' directory, just to confirm) that needs to not be rewritten but is being rewritten. The file is: ShippingZZencart.php from stamps.com
I thought the last lines of the htaccess were to prevent rewriting real files but they don't seem to be. This is the htaccess file contents.
###############################################################################
Common directives
###############################################################################
NOTE: Replace /shop/ with the relative web path of your catalog in the "Rewrite Base" line below:
Options +FollowSymLinks
RewriteEngine on
RewriteBase /store/
###############################################################################
Start Ultimate SEO URLs
###############################################################################
Handles the new URL formats
RewriteRule ^(.)-c-([0-9_]+)/(.)-p-([0-9]+)(.)$ index.php?main_page=product_info&products_id=$4&cPath=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-c-([0-9_]+)/(.)-pi-([0-9]+)(.)$ index.php?main_page=popup_image&pID=$4&cPath=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-c-([0-9_]+)/(.)-pr-([0-9]+)(.)$ index.php?main_page=product_reviews&products_id=$4&cPath=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-c-([0-9_]+)/(.)-pri-([0-9]+)(.)$ index.php?main_page=product_reviews_info&products_id=$4&cPath=$2&%{QUERY_STRING} [L]
Original (unchanged) URL formats
RewriteRule ^(.)-p-([0-9]+)(.)$ index.php?main_page=product_info&products_id=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-m-([0-9]+)(.)$ index.php?main_page=index&manufacturers_id=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-pi-([0-9]+)(.)$ index.php?main_page=popup_image&pID=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-pr-([0-9]+)(.)$ index.php?main_page=product_reviews&products_id=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-pri-([0-9]+)(.)$ index.php?main_page=product_reviews_info&products_id=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-ezp-([0-9]+)(.)$ index.php?main_page=page&id=$2&%{QUERY_STRING} [L]
RewriteRule ^(.)-c-([0-9_]+)(.)$ index.php?main_page=index&cPath=$2&%{QUERY_STRING} [L]
All other pages
Don't rewrite real files or directories
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?main_page=$1&%{QUERY_STRING} [L]