FFT Megafunction problem - strange spikes

I am still trying to understand your problem. Is it both matlab and fpga showing same problems or just fpga. I can see your spikes are very low pointing to some quantisation issues.

Yes you are right your cycles are complete, sorry. Also try better bitwidth resolution, you are only using max value of 256.

can you also focus on differences of real and imag between fpga and matlab and not the abs of fft since you are adding further processing.

In your matlab program you are rounding x but you are not rounding fft result.