Hi,
As IOhannes pointed it in this Github pull request ( https://github.com/pure-data/pure-data/pull/81), the FFT functions in d_fft_fftsg.c are not thread-safe. An easy fix would be to set the static variables TLS (*PERTHREAD*). (It doesn't solve the "size problem" of the original pull request but it can be complementary). If it seems good for you, I will add this to the pull request dedicated to the multi-instance/multithreading problems on Github ( https://github.com/pure-data/pure-data/pull/288).
Another solution would be to integrate these static variables in the pd instance structure (and to allocate the memory for each instance)? Nevertheless, this second solution would add some code pretty useless if someone use the FFTW wrapper. But is anybody using the FFTW wrapper (d_fft_fftw.c)? If this second solution seems more suitable, I can create a new pull request.
Cheers, Pierre