Quartus FFT IP output problem

hi,

I use the FFT IP from Quartus 6.0 with 16 bits input data and 16 bit
twiddle and 1024 pts in streaming data flow

Before sending data to the FFT I make a flat top window on my samples

My frequency sampling is 10 MHz and I send a pure 1MHz sinus to the
real input, with 0 to the imaginary input...

When I compute Re[X]^2+Im[X]^2 (magnitude squared) I see an
amplitude variation on this output from a FFT result to another FFT
result, there's an amplitude modulation on my output...

Do you know if you have already notice this ?

Thanks