Steps to reproduce the issue

1. Run the attached design through Yosys flow - works fine
2. Run PNR of the EDF file created by Yosys on SpDE - works fine
3. Run Simulation - Fails
4. Run the FPGA register access test on the board - fails

Expected behavior

write the register (0x40020804) = 0x87F
Read the register (0x40020804) expected result = 0x87B

Actual behavior

write the register (0x40020804) = 0x87F
Read the register (0x40020804) actual result = 0x873

Please describe how the behavior you see differs from the expected behavior.
We see the bit[3] of the register (which is RX FIFO Full Interrupt Enable) = 0 even though it is set to 1.

one observation:
In this design there is a register bit which has the asynchronous set and Async reset, if I change that
register to remove the async set then the register access works fine.

"always @( posedge WBs_CLK_i or posedge WBs_RST_i or posedge DMA_done_i)
begin
if (WBs_RST_i)
begin
DMA_Done_IRQ <= 1'b0;
end
Test_design9.zip
Test_design9.zip

else if (DMA_done_i)
	DMA_Done_IRQ    	     <= 1'b1;
else
begin
	if ( (VGA_DMA_CTRL_Wr_Dcd && WBs_BYTE_STB_i[0]))
    begin
       DMA_Done_IRQ   <=  WBs_DAT_i[2];
    end
end  

end "