Build system supports fftw v2 only.
This is already in the dedicated Feature Requests ticket tracker:
Work is in progress at the moment to remove FFTW2 and replace it with FFTW3 (either in the main distro or as a separate d/l from CPAN). See pdl-porters list archives for 2013-August. For now you can try it out from GitHub: https://github.com/dkogan/PDL-FFTW3.