We have tested both the bitstream file and MATLAB BSP, it seems the problem has been solved both for RevE and RevF.
Just one remark: the pin name in top level VHDL file is not exactly the same as the definition in NGC file generated from MATLAB BSP. "ce_1" -> "ce" and "clk_1" -> "clk";
Thank you, Pat, for the time and efforts you made with this issue.
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