factor-bundle creates broken bundles when required modules have linked dependencies. This happens for example when installing moment-timezone and afterwards moment. So moment exists two times in the node_modules folder, once for moment-timezone and once in moment. This seems to break browserify. When installing the modules the other way around the bundle does not break (this time there is only one moment).
I don't know if this is more of a problem with the way npm install modules when they have duplicate dependencies or if this is a problem with factor bundle.
I set up a test case over at: https://github.com/davidlanger/factor-bundle-moment-timezone