Hi Dmitry,
What is the wrong value that is read after the linux kernel boots. Is is 0x00000000.If you are reading zeros, it could be likely that the EMIFA is LPSC clock gated. Can you check after the linux boot if the power domain for EMIFA is on.
Do you have asynchronous memory connected to the EMIF that may be initialized from the kernel?
Regards,
Rahul