I have partially tracked it down.
Writing the patch I made the assumption (without checking the code: very bad ;) ) that sys.path is set to []
in the frozen code case. This is false in general. 
But there are also other related/similar potential bug in the preexistent code.
There is also a bug in jythonc which passes a null frozenPackage param.
 
I will track these issues completely and make the necessary fixes.
 
regards, Samuele.