When I load the app from the root directory of my server the app works. This is not possible in practice because of the pretty urls our application uses. For example http://www.website.com/modules/worker/person/1/1/1 loading a page with the previous url results in system.js looking in the folder /modules/worker/person/1/1 rather than a folder based on "/".
The solution is to set baseURL:"/" such that the modules are loaded based on the root directory.
The problem with THIS solution is that node modules are not loaded properly, instead of looking in the node_modules directory, system.js is looking in the root. system.js looks in /angular2/http.js rather than /node_modules/angular2/http.js
When I switch from "node" module compilation to "classic" the result is the same.
Any thoughts on how to proceed?
System.confighere as an answer. It could be helpful for next developers.