FFT problem. Simulation vs HW's execution

Before we blame fft core we must make sure the whole input frames are same to all 4 ffts. Don't just compare four different results with sim results as this could be misleading. Are you sure the fifos are getting data correctly? Or can you just look at whole frames at inputs/outputs of fft directly and not just few samples. Is start of frame ...etc all correct as well. If your clock is variable I take it you have constrained for fastest case.

If indeed you inject same input frames into same instants of fifos and you get different results then I will blame fifos. If however you get good results by lowering frequency then something else is wrong such as timing or your control signals logic.