When your application starts it checks for whether or not Friendly URLs have been correctly configured on the web server by pinging a special URL for a response:
If friendly URLs are not working on server restart, but
/pingFU works successfully, it's possible that the
pingFU check itself is failing temporarily on server restart. This can happen if your server is slow or in some security configurations.
You can force friendly URLs to be always on by activating the Friendly URL service with a config on application start.
Edit your project's
/projects/yourProjectName/config/_serverSpecificVarsAfterInit.cfm config and add the following line of code anywhere in that file:
<cfset application.fc.factory.farfu.turnon() />
Now restart the app and it should be in place.
Copious amounts of detail on Friendly URLs, and how they can be activated for a multitude of environments is available on the FarCry WIKI: