If you read carefully, everything works fine if we use bios version 0049 or 0046 ( that is what I used before ) the problem shows up if one updates the bios to verison 0052.
We have over 30 machine using this board with version 0049 with no problem (debian installed to, and booting from integrated eMMC).
We need this update because it fixes an issue that 0052 solves as mentioned in the release notes;
extract from release notes : "Fixed an issue where executing a reboot or shutdown -r command in Linux, the system would hang." .
For us it means that the customer has to pulled the plug instead of cleanly powering off the machine, and customer does not like to see a frozen system...