Flash-Problem Nios IDE 9.0 SP2

I have some problems while trying to flash my epcs and flash.

if i try to program my epcs with the sof and a nios2 IDE programm some pins within the design change. It's always the DDR2 pins and always the same pins.

We have a costum FPGA board and use an own .xml file for the ddr2 high def IP-Core. i have to reload the xml file before recompiling the sopc-builder or else the pins stay changed.

Do i have to change some settings so that it will always load our custom xml?

why can the flash-programmer change pin settings? :confused: