Yes, kaz. That is exactly what I am saying. Matlab fft and testbench (both my own and the altera generated matlab testbench) work perfectly ok. The hardware does not, though. but I am now finding out that when I clock the FFT core at frequencies less than or equal to 10MHz, the output is correct ! I am still doing some tests to see if this works over the entire dynamic range. I will keep the thread posted but I suspect that the FFT core (in my cyclone II device) cannot be clocked too fast.
This actually will cause a problem for me because I will need to change the clocking of my ssram (one frequency during acquisition, and another frequency during FFT), which means I might have to use a gated clock :(