My install is pretty much vanilla Python 3.0.1. All I changed was the line added to ~/.bash_login by the Python installer. Notice that ${PATH} is before the path to the Python 3.0.1 binary files:

# Setting PATH for MacPython 3.0

# The orginal version is saved in .bash_login.pysave

PATH="${PATH}:/Library/Frameworks/Python.framework/Versions/3.0/bin"

export PATH

When running this tiny program I get the expected output:

#!/usr/bin/env python3.0

print ("hallo world")

It really doesn't matter if you use Python 3 as the default version of Python or not, so there must be something that you changed. AFAIK, the only change that you really needed to do is either run the command file from the Python 3.0 folder or add those 4 lines in the .bash_login file (or whatever shell you use).