Issue of this bug is that most part of fftw is not thread safe, only compute-intensive fftw_execute & co are threadsafe.
Since I realized smoke was affected by this issue as well, I had to add an helper fftw_threadsafe_private.h/.c file in BKE, hope this is OK.
Audaspace also uses fftw in one of its readers (AUD_BandPassReader.cpp), but this is not an issue currently since this code is disabled in CMake/scons files.
Note I also ran into another threading issue with smoke, and had to copy dm used by emit_from_derivedmesh() func,
not sure this is a nice solution but at least it works and should be reasonably safe!