Comment 33 for bug 136252

The problem would appear to be in the --incremental flag, it is unable to create the map file for the arrays already created and mdadm gets confused. A quick fix is to add this to the mdadm hook in initramfs:

# Create runtime directory for incremental map
mkdir -p ${DESTDIR}/var/run/mdadm

My machine still doesn't activate lvm properly though, but that would be a different issue =)