I just built Loris-1.8 (on Mac Snow Leopard) and had a problem building the utilities. ./configure detected fftw3, but the link flag wasn't being passed to g++. The generated g++ command was (within utils dir)
g++ -I../src -m32 -o loris-analyze loris_analyze-loris_analyze.o -Wl,-bind_at_load ../src/.libs/libloris.a -lm
which failed because the linker couldn't find fftw3 symbols.
Attached is a modified utils/Makefile.am which includes the $(LINK_FFTW) flags for all utils. After an autoreconf I successfully built loris, the utilities, and the csound and python interfaces.