I downloaded the barebone example of Twitter\'s bootstrap and customized it. I tested it locally (with WAMP server) and everything works perfectly, both the CSS and the JScr
Back to basics: If Debug is set to true on the local machine and false on the deployment environment as it should be, make sure your .min.js files are not overriding customizations you have made to the non-minified versions of .js files (applies to .css as well).
You can also turn Debug off on the local machine and you should see the same issues.