I had a similar issue here using systemd-208 with kernel 3.13.1 and 3.14.4 under Exherbo (similar to Gentoo): my separate partitions (/var, /home, /boot and even /swap) were mounted under the desired root location. Everything worked fine. Then, upgrading to systemd 213 the boot process stopped at the point, where the partitions should have been mounted with the message: 'A start job is running for dev-sdxx.device' until timeout of 1 min 30 sec. Afterwards I was in Emergency Mode. Excerpt of
$ journalctl -xb
Jun 09 13:50:29 exathlon systemd[1]: Job dev-disk-by\x2dlabel-BAK_A4.device/start timed out.
Jun 09 13:50:29 exathlon systemd[1]: Timed out waiting for device dev-disk-by\x2dlabel-BAK_A4.device.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /mnt/BAK_A4.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for Local File Systems.
Jun 09 13:50:29 exathlon systemd[1]: Triggering OnFailure= dependencies of local-fs.target.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /export/LinuxMint13_KDE_64.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /export/SystemRescueCD-x86.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for File System Check on /dev/disk/by-label/BAK_A4.
Jun 09 13:50:29 exathlon systemd[1]: Job dev-sdb11.device/start timed out.
Jun 09 13:50:29 exathlon systemd[1]: Timed out waiting for device dev-sdb11.device.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /var.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for Update UTMP about System Boot/Shutdown.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for Load/Save Random Seed.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for File System Check on /dev/sdb11.
Jun 09 13:50:29 exathlon systemd[1]: Job dev-sdb8.device/start timed out.
Jun 09 13:50:29 exathlon systemd-journal[1044]: Forwarding to syslog missed 15 messages.
Jun 09 13:50:29 exathlon systemd[1]: Timed out waiting for device dev-sdb8.device.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /home.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for File System Check on /dev/sdb8.
Jun 09 13:50:29 exathlon systemd[1]: Job dev-sda6.device/start timed out.
Jun 09 13:50:29 exathlon systemd[1]: Timed out waiting for device dev-sda6.device.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /boot.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for File System Check on /dev/sda6.
Jun 09 13:50:29 exathlon systemd[1]: Job dev-sdb5.device/start timed out.
Jun 09 13:50:29 exathlon systemd[1]: Timed out waiting for device dev-sdb5.device.
Jun 09 13:50:29 exathlon systemd[1]: Dependency failed for /dev/sdb5.
shows the failed attempts of mounting by systemd.
After looking up the internet I was able to find a remedy in configuring the kernel with
CONFIG_FHANDLE=y (before: n)
see 'systemd System and Service Manager' under
REQUIREMENTS:
CONFIG_FHANDLE (libudev, mount and bind mount handling)
source: http://cgit.freedesktop.org/systemd/systemd/tree/README
Afterwards the problem was solved, all partitions mounted again.
I cannot tell, why this was not happening / or was not required with systemd 208.