Can you compile the ATLAS lib locally? And then use the install script. My solution was to always use standard directories.
See also that the .so files are symbolic links to the .so.3.2.1 libs.
It seems that you are missing a dependency. The FFTW3 is missing.
helio@linux-techno:/usr/lib64> l *lapack*
-rw-r--r-- 1 root root 20018986 Jul 5 2010 liblapack.a
-rw-r--r-- 1 root root 20302074 Jul 5 2010 liblapack_pic.a
lrwxrwxrwx 1 root root 18 Out 4 2010 liblapack.so -> liblapack.so.3.2.1*
lrwxrwxrwx 1 root root 18 Out 4 2010 liblapack.so.3 -> liblapack.so.3.2.1*
-rwxr-xr-x 1 root root 5308064 Jul 5 2010 liblapack.so.3.2.1*
helio@linux-techno:/usr/lib64> l *blas*
-rw-r--r-- 1 root root 1471064 Jul 5 2010 libblas.a
-rw-r--r-- 1 root root 1477384 Jul 5 2010 libblas_pic.a
lrwxrwxrwx 1 root root 16 Out 4 2010 libblas.so -> libblas.so.3.2.1*
lrwxrwxrwx 1 root root 16 Out 4 2010 libblas.so.3 -> libblas.so.3.2.1*
-rwxr-xr-x 1 root root 362648 Jul 5 2010 libblas.so.3.2.1*
lrwxrwxrwx 1 root root 20 Out 4 2010 libgslcblas.so.0 -> libgslcblas.so.0.0.0*
-rwxr-xr-x 1 root root 215120 Jul 5 2010 libgslcblas.so.0.0.0*
lrwxrwxrwx 1 root root 16 Out 4 2010 liblash.so.2 -> liblash.so.2.0.0*
-rwxr-xr-x 1 root root 52392 Jul 5 2010 liblash.so.2.0.0*
helio@linux-techno:/usr/lib64> l *fftw*
lrwxrwxrwx 1 root root 18 Out 4 2010 libfftw3f.so -> libfftw3f.so.3.2.4*
lrwxrwxrwx 1 root root 18 Out 4 2010 libfftw3f.so.3 -> libfftw3f.so.3.2.4*
-rwxr-xr-x 1 root root 1019824 Jul 5 2010 libfftw3f.so.3.2.4*
lrwxrwxrwx 1 root root 26 Out 4 2010 libfftw3f_threads.so.3 -> libfftw3f_threads.so.3.2.4*
-rwxr-xr-x 1 root root 27168 Jul 5 2010 libfftw3f_threads.so.3.2.4*
lrwxrwxrwx 1 root root 17 Out 4 2010 libfftw3.so -> libfftw3.so.3.2.4*
lrwxrwxrwx 1 root root 17 Out 4 2010 libfftw3.so.3 -> libfftw3.so.3.2.4*
-rwxr-xr-x 1 root root 1048488 Jul 5 2010 libfftw3.so.3.2.4*
lrwxrwxrwx 1 root root 25 Out 4 2010 libfftw3_threads.so.3 -> libfftw3_threads.so.3.2.4*
-rwxr-xr-x 1 root root 27160 Jul 5 2010 libfftw3_threads.so.3.2.4*
helio@linux-techno:/usr/lib64>
Hope it helped.
(my Linux is OpenSUSE and I am having trouble with gtk/glib, gretl_x11 crashes :( )