We have a server setup as follows:
NOTE: Question above includes a solution as well.
I think this is an error with the Coldfusion Connector. I would post a bug report to Adobe (https://bugbase.adobe.com/). I do have a workaround though. I have the same issue, but I use IIRF (Ionic IIS Redirector - http://iirf.codeplex.com/), and I found a way to use that to avoid the bug for now:
In the IirfGlobal.ini file (normally located in C:\Windows\System32\inetsrv\IIRF), add the following line:
RewriteFilterPriority HIGH
This will allow IIRF to handle 404 requests before it even hits ColdFusion/Tomcat.
In the site-specific Iirf.ini (usually you create one in the root folder of your web files -- see the IIRF docs for details), add the following rules:
RewriteCond %{SCRIPT_TRANSLATED} !-f
RewriteCond %{SCRIPT_TRANSLATED} !-d
RewriteRule ^(.+)$ page_to_redirect_to.cfm?404;$1 [L]
That will redirect all files/directories that don't exist to page_to_redirect_to.cfm, and add the 404 query string like normal.
EDIT: Added a following step: Go into the IIS Manager and select either the server or the Web Site that was configured to use IIRF, then go into the ISAPI Filters section. Click on "View Ordered List", then move the IIRF filter up to the top.
EDIT 2: Just posted a bug to Adobe. See https://bugbase.adobe.com/index.cfm?event=bug&id=3630245
Hope that helps.