[eluser]vbsaltydog[/eluser]
Enable the logging in CI
Start with a clean CI logfile
Do a single request of a CI page
Examine the CI logfile and see if there was more than one execution of CI
If there was more than one CI execution then look at the page source in the browser for a resource that was loaded by the server and was rewritten to index.php but not found as a controller/method.
Ex.
Your source code includes a call to a js file but it doesn't exist on your server so your htaccess rule sends anything that is not a valid dir/file with the -d -f rules to index.php
index.php sends the js file to CI as a route but there is no such route.
There would be two CI executions, one for the initial URL and one for the js file, the initial call would show the page in the browser but the secondary call for the js file would return the 404 header.