Dmitry,
I'm finding something similar in my environment. I find that as a workaround I can touch /efi/boot/bootx64.efi on the ESP and the entries are no longer corrupted after rebooting when viewing from efibootmgr. Can you see if maybe that helps to workaround it for you too?
Also, by chance do you have an /efi/boot/bootx64.efi on some other partition on the disk too? I'm wondering if that might be causing the BIOS to flag a different partition as the ESP.