FFT Megafunction problem - strange spikes

When you compare Matlab fft with fpga fft you should quantise Matlab model in a way similar to fpga.

fft inputs: you need to input into Matlab and fpga the same quantised input and that is what you are doing I believe.

fft outputs: Similarly you need to compare like by like i.e. quantised Matlab fft output with fpga fft output. Moreover, you better check real and imaginary outputs rather than abs() since this adds further processing.

Then you and we can come to some better idea what the error is. If yoy then have fpga spikes then they should be +/- few integer values for a quantised range. Let us know...