Why is the first data frame after a multi-cycle reset incorrect?
This is a known problem, where the first frame of data is incorrectly marked as valid. To work around this issue, you can ignore the first frame after the reset.
This issue has been resolved in the xFFT v4.0, which was released in December 2006.
See (Xilinx Answer 29209) for a detailed list of LogiCORE Fast Fourier Transform (FFT) Release Notes and Known Issues.