The problem was in my metamodel URI. The metamodel was defined using ecore, you should always put "http://" in front of the metamodel URI!
The name of my metamodel was: org.colpaert.mathias.PSMAndroid, it is was imported in my acceleo module as following:
[module model('org.colpaert.mathias.PSMAndroid')/]
This caused acceleo to look for the metamodel in a path relative to the module file. In a standalone, after compilation, this is just the /bin folder.
I changed my ecore metamodel URI, regenerated the genmodel (etc). Next I changed the acceleo module to:
[module model('http://org.colpaert.mathias.PSMAndroid')/],
Cleaned the solution, recompiled and it worked.
Big thanks to Stéphane Bégaudeau, he solved this here (its in french)