Hi Arashaz,
Take a look in PORBMSR register (in ROM_LOC field more exactly) to see which is right now the default rom_location set it up now by the FPGA code (having no DIP SW on the board is pretty sure that the cfg_rom_loc is driven by FPGA).
You can't use PMUXCR register from software (this is fully focus on soc level muxing, not for POR stuff which are read-only).
Basically, you have 2 options:
1. use the flash/boot method suggested by cfg_rom_loc from PORBMSR........or
2. update the FPGA to use your specific cfg_rom_loc (I'm not familiar with FGPA code -- maybe a hardware guy can help on this side).
Regards,
Marius