Altera FFT Vs Matlab FFT. Strange Results

Already done.

My design has 3 IP cores: two FFT and one IFFT. One FFT has as input the pseudorandom code; the second fft some bpsk signals. After some products in frequency domain i come back in time domain to check data messages. Using a Lut instead of the FFT (with the matlab ffts with 12 bit fixed points) for the pseudorandom codes every things is ok. If i replace the LUT with the FFT from Altera for the pseudoradom codes the results are not correct. The second FFT and the IFFT are Altera IP FFT cores and work perfectly. The problem is the FFT for this particular input (only {-1,1}).

An independent design check comes from the matlab test bench after generating the core (page 2-16 FFT MegaCore function V8.0 User Guide).

Thanks