Just to add another data point, I ran into the same problem. Booting stops with
ALERT! /dev/mapper/vgsys-sid--usr does not exist. Dropping to a shell.
In busybox I can fix the problem by activating the volume groups:
(initramfs) vgchange -a y 30 logical volume(s) in volumgroup "vgsys" now active
Hitting Ctrl-D afterwards resumes the boot. For some odd reason, it notices that /usr has been mounted 922 times without being checked and forces the fsck. I never checked (nor do I really care, /usr can be recovered from ftp.debian.org).
The version of initramfs-tools on my system is 0.117 as well. I would consider this as serious since that system booted just fine since its installation in 2009, not counting the systemd transition which made it unbootable two times.
I attached the trace.log from running mkinitramfs. Greetings, Torsten
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trace.log.xz
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