This issue seems to be related to new DDR3 training code in the new firmware. It seems that Marvell, the manufacturer of the Armada 385 SoC in Turris Omnia, has broken their DDR3 training code several years ago and has been unable to fix the issue still.
I have been working on a solution where both the old and new DDR3 training implementations will be built into the U-Boot bootloader, and users experiencing these issues will be able to tell U-Boot to use the old code via one command and a reboot.
It should be available today, I will give information on how to try it later.