Is there any chance that SciPy was compiled without the ATLAS/BLAS/LAPACK libraries? (You can verify this using with the "numpy.show_config()" and "scipy.show_config()" functions in an interactive python session.) In that case, all the numerical math would be done in straight Python rather than optimized C/FORTRAN.
ATLAS/BLAS/LAPACK is mostly useless for basic sparse operations, at least in scipy. It becomes useful for more advanced operations like SVD, etc... Unless you can use dot (scalar product), which is very fast in numpy if you use atlas (e.g. time the difference between np.sum(x * x) vs np.dot(x, x) - sum does not use atlas, dot does).
For sparse SVD as I implemented in scipy, even fast dot does not seem to make that much of a difference (would be interesting to do real benchmarks, though).
