While testing with SD3 which board did you use?
Are you getting any errors in the UART prints?
Thanks for the quick reply. We have a custom board for SD3, and follows almost exact schematic as FX3S DVK. Upon further investigation, we found that the orientation of eMMC was wrong! So making it right would hopefully fix it. We will make new boards with right orientation, check it again, and update here if any problem occurs. Meanwhile we can consider this solved.