Hmmm... I wonder if your old URL rewrites were doing something funky then?
I usually use this for Apache mod_rewrite:
RewriteEngine On
RewriteCond %{REQUEST_URI} !(^/farcry|^/webtop|^/flex2gateway|^/flashservices|^/CFIDE)($|/)
RewriteRule ^([a-zA-Z0-9\/\-\%:\[\]\{\}\|\;\<\>\?\,\*\!\@\#\$\ \(\)\^_`~]*)$ /index.cfm?furl=$1 [L,PT,QSA]
and this for IIS Rewrite in IIS 7.x (using the import option):
RewriteCond %{REQUEST_URI} !(^/farcry|^/webtop|^/flex2gateway|^/flashservices|^/cfide)($|/)
RewriteRule ^([^\.]+)$ /index.cfm?furl=/$1&%1 [L,PT,QSA]
The "QSA" means "query string append" which means any existing query string variables should make it through to the rewritten URL.
cheers,
Justin