I had a similar error a little while ago, and I got around it by recompiling the problem package with the new numpy/scipy already installed. I also had a possibly related problem with getting bus errors on import that went away after I recompiled the packages except in the case of Matplotlib, which I had to revert to v.98.

Message: 2
Date: Thu, 10 Sep 2009 12:29:47 +0000 (UTC)
From: Dave <dave.hirschfeld@gmail.com>
Subject: [SciPy-User] scikits.timeseries  ImportError
To: scipy-user@scipy.org
Message-ID: <loom.20090910T142853-384@post.gmane.org>
Content-Type: text/plain; charset=us-ascii

I decided to try installing the latest scipy/numpy which seemed to work fine but
afterwards I got an import error when trying to import the timeseries module.

Upgrading my timeseries to the latest:

M:\src\timeseries>svn up
Fetching external item into 'scikits\timeseries\doc\
sphinxext'
External at revision 7375.
At revision 2216.

Still resulted in the same error:

Python 2.5.4 (r254:67916, Dec 23 2008, 15:10:54) [MSC v.1310 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
|>>> import numpy
|>>> numpy.__version__
'1.4.0.dev7375'
|>>> import scipy
|>>> scipy.__version__
'0.8.0.dev5920'
|>>> import scikits.timeseries as ts
RuntimeError: FATAL: module compiled aslittle endian, but detected different
endianness at runtime
RuntimeError: FATAL: module compiled aslittle endian, but detected different
endianness at runtime
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "C:\dev\bin\Python25\Lib\site-packages\scikits\timeseries\__init__.py",
line 13, in <module>
   import const
 File "C:\dev\bin\Python25\Lib\site-packages\scikits\timeseries\const.py", line
79, in <module>
   from cseries import freq_constants
ImportError: numpy.core.multiarray failed to import
|>>>

Whereas from the interpreter it appears to work:

|>>> import numpy.core.multiarray
|>>>

cseries appears to be a C file so I'm a bit stumped as to how to debug further.
Any help appreciated!

Thanks,
Dave