Pre-program with BP Microsystems Programmer a device Altera 10M08SAU169C8G

SMTC is using the Altera 10M08SAU169C8G

Here I have an issue to pre-program the part with BP Programmer. (Prior to install on a PCB)

I have two options:

Option1 is to pre-program the device at BP Programmer.

Option2 is to program the device on board using the Quartus JTAG programmer.

In both options I use the same .pof file.

When I pre-program the device with BP Programmer the units PCBAs do not work, they did not boot.

When I program the device with Quartuz JTAG programmer the units work correctly.

Could you, please help me?

I need to know if Quartus perform something else at the end of programming the device.

Regards