Did you install python by hand (compile + install) or via a package? If you installed by hand, maybe reinstall?
Running ldd on the numpy .so files might yield interesting results. Is it pointing to libraries the same place as running ldd on cvfilter_py.so?
Do you have multiple versions of numpy installed (eg, python2 and python3?). Maybe get rid of one of them.
It would be interesting to know the contents of sys.path when the numpy import occurs. You can do this by inserting this before the numpy insert fails:
Code:
PyRun_SimpleString("import sys; print(sys.path)");