MAX 10 program failure

I have a cutomized MAX 10 board with 10M08DAF256C8G FPGA chip. I experienced repetitive program failure with sof file and Quartus 16.0. The first few times program failed with "Error (209014): CONF_DONE pin failed to go high in device 1. Make sure all communication cables are securely connected, select a different device, check the power on the target system, or make sure all nCE pins are connected to GND.

Error (209012): Operation failed

". Then programming 100% successful, but the first time successful is not a real success since SignalTap cannot detect the instance and program is not working on the board (I have a LED indicator on the board), the second time is a real success. I did some search and tried Quartus 18.0 programmer which works much better and didn't see programming failure, but the first time success still is not a real success. This seems like to be a Quartus issue. Any work around on Quartus 16.0? Thanks