Did you run the deployment by hand, or have CIM do it?
I've seen a minimal Endeca app created when I incorrectly specified the deployment template. Once, for example, I typed "-app" rather than "--app" (one dash rather than two) as a deploy script argument. The deploy script seemed to run correctly and it did create an application... but it lacked all the specifics added by my deployment template (including scripts like set_media).
I faced the same. My issue was in using gs.zip (Oracle Endeca Guided Search) as Tools and Frameworks. I stoped this service and uninstalled it. Then installed xmgr.zip (Oracle Endeca Experienced Manager) and ran it. After that I got back to CIM and continued CRS deploying. But faced that can't deploy an app with name CRS because it already exists. So I added <arg value="--force" /> to ATG/CIM/plugins/Base/ant/cim-ant.xml in 865 line. Then all work fine.
I've found out that for some reason endeca config at %DYNAMO_HOME%\servers\[INSTANCE_NAME]\localconfig\atg\endeca\ApplicationConfiguration.properties was corrupted. Here is my current config, it might be helpful:
Make sure that in this file you specified properties that were specified in CIM.
Important! Check this config BEFORE initializing your Endeca application. Just exit CIM after DB and server instances configuration, check config file and then run CIM again and create your Endeca application (as described in CRS Installation and Configuration Guide).