Comment 2 for bug 1495873

Have you changed something else about initramfs-tools? Files in /usr/share/initramfs-tools/scripts/ are not normally run at update-initramfs time; they run in the context of the initramfs, and in that context, the path starting with /root is perfectly correct.

Can you please investigate and find out why that script is being run at all at update-initramfs time for you? It really shouldn't be.