What exactly was the option letting you select a custom initrd? This
doesn't seem to be a question that comes from the initramfs-tools
package.
After reinstall, did you use the same syntax in /etc/crypttab? I think
the issue here is that the cryptdisks-udev job handles UUID=, LABEL=, or
/dev/sd* as source devices, but is not configured to handle /dev/disk
/by-id. So this device will only be brought up if it's caught by the
cryptdisks-enable catch-all job, which is racy.
** Changed in: cryptsetup
Status: New => Invalid
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crypttab entries not processed automatically at startup despite upstart files
https://bugs.launchpad.net/bugs/522341
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