this is expected behavior, flash-kernel 3.x now reads from /usr/share
/flash-kernel/bootscrpts/* and also does not require a root= line
anymore (this is hardcoded in the initrd at install and updateinitramfs
time) ... i guess technically flash-kernel should migrate the old boot
scripts over but sadly there is no mechanism for user created boot.scr
files to override the packaged ones atm.

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https://bugs.launchpad.net/bugs/1026780

Title:
  3.0~rc.4ubuntu4 doesn't honor bootargs from /boot/boot.script anymore

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