FFT Megacore V11.1 problem

If captured data from ram is captured at the point it goes into fft inside fpga then I will say so far so good.

Then if it timing problem I expect the tool to report violations but I doubt it because I can assume that timing violations may be random and not leading to regular harmonics. At first I thought may be some MSBs are violated but then I expect chaotic output unless it involved some corner coefficient only.

You may run at 1 MHz with full dynamic range and see. Also apply reset just in case.