FFTW doesn't build universal without a lot of work. The problem is that it adds optimization flags per processor, even in a "portable" configuration, and -arch flags don't make a difference.
Rather than spell out the whole mess, these instructions are for a single native architecture build. See the framework build script for all the gorey details. Note that fftw includes it's own copy of the blas library, the build script hacks the source to use the OSX copy of blas in the vecLib framework.
In the fftw source folder:
./configure --enable-threads --enable-shared --disable-static \ --disable-dependency-tracking --disable-fortran --with-combined-threads make sudo make install