Hey I recently redid our site with modrewrite URLs and had your same question.
None of the urls to be rewritten were real directories, so if yours is the same, you can do what I did and exclude all real directories from the rewrite and then remove any trailing slashes (put this before your rewrite rules begin):
Code:
# Do not rewrite real directories
RewriteCond %{REQUEST_FILENAME} !-d
# Remove trailing slashes
RewriteRule ^(.*)/$ /$1
Not sure of your exact situation or if this will work for you, but I hope it helps.