Hi nija_manko,
Sorry for my late response I was sick the last weeks and just recently come back.
I review the boot configs and the memory you are using, there are a few things that come to my mind to debug this, usually is because the memory uses a different work voltage than the one you are using, from what I see this is correctly configured, according to the schematics you share, but we could try to move the BOOT_CFG[1] that change the operating eMMC voltage.
Other stuff that probably is causing this and we could try:
1. reason may be poor soldering, one can resolder eMMC or change from a known good board.
2. one can debug it using an oscilloscope or digital analyzer and sect.7.4.2 Operating voltage range validation eMMC specification:
http://yourcmc.ru/wiki/images/5/55/EMMC_JESD84-A441.pdf
https://community.nxp.com/thread/341480
If there is something more I can do for you, please let me know.
Regards,
Israel.