Cyclone V does not boot from S25FL128 if SOF2FLASH is used

I've actually found the problem.

The issue was that sof2flash utility could not generate proper srec file. Either the little-endian format was wrong or there were wrong bytes in header area.

To resolve this issue I used a third party utility https://sourceforge.net/projects/srecord/ to convert .rbf file into .flash

The command line for this is

srec_cat file.rbf -Binary −Bit_Reverse -Output=file.flash 

-Binary option specifies that input file has binary format

and

- Bit_Reverse option specifies reversing bits in output file.

With this command a proper .flash file can be generated, which then can be programmed using nios2-flash-programmer or quartus_pgm into Flash.