I've seen this error orfor a multitude of reasons, none of which have anything to do with the fact that it says bin/bin, which is a bit of a misleading message. As Nuno comments its a general CD configuration issue, nothing specific to the Reference Implementation. Did you already have a working CD environment? It could be an invalid or missing license, missing jar files in your bin/lib directory, or even Java compatibility issues - I have only used the Reference Implementation with Java 7 - if you are not using this version, it may be that there is some compatibility issue with tridion or 3rd party jars in the example web app, or loaded from somewhere your CLASSPATH (if set).