The problem was that the new motherboard's BIOS created a host protected area (HPA) on some of the drives, a small section used by OEMs for system recovery purposes, usually located at the end of the harddrive.

ZFS maintains 4 labels with partition meta information and the HPA prevents ZFS from seeing the upper two.

Solution: Boot Linux, use hdparm to inspect and remove the HPA. Be very careful, this can easily destroy your data for good. Consult the article and the hdparm man page (parameter -N) for details.

The problem did not only occur with the new motherboard, I had a similar issue when connecting the drives to an SAS controller card. The solution is the same.