Hmm.  I don't see any difference between the two here (OS X 10.6).  What platform are you on, and where did your copy of Python 3.1.2 come from?

newton:~ dickinsm$ cat test.py
import sys
print(sys.argv[1])
newton:~ dickinsm$ python3.1 test.py 1234
1234
newton:~ dickinsm$ python2.6 test.py 1234
1234
newton:~ dickinsm$ python3.1
Python 3.1.2 (r312:79147, May 18 2010, 17:21:15) 
[GCC 4.2.1 (Apple Inc. build 5659)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 
newton:~ dickinsm$ python2.6
Python 2.6.5 (r265:79063, May 18 2010, 17:12:15) 
[GCC 4.2.1 (Apple Inc. build 5659)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>