Make sure the .sof file programmed to your device is the updated one with new .stp added to your project. You need to add .stp file before compile and build the new project (new.sof). Make sure the OS meet the Quartus requirement as sometime this might be causing the issue.
I also found similar to your issue. Can refer to link below for details
I make sure select the right stp file and recompiled the project.
Now，it seems like I just reprogram the board with my own .SOF file，and then the FPGA load the file in the flash immediatetly.