I've investigated the issue and it looks it's not a initramfs-tools package problem but mountall problem.
There is a file /lib/init/fstab from that package that has configuration lines with /var/run and /var/lock.
It seems that one who has /var on separate partition should put lines for 'run and 'lock in his /etc/fstab to override the /lib/init/fstab lines.
There should be some documentation, guide for users- then this "bug" would be partially solved.
I've investigated the issue and it looks it's not a initramfs-tools package problem but mountall problem.
There is a file /lib/init/fstab from that package that has configuration lines with /var/run and /var/lock.
It seems that one who has /var on separate partition should put lines for 'run and 'lock in his /etc/fstab to override the /lib/init/fstab lines.
There should be some documentation, guide for users- then this "bug" would be partially solved.