I have a similar problem with /etc/rc.local starting uninterruptible power 
supply monitoring software at boot.
Up to ubuntu 8.10 it would start automatically when I edited the rc.local file. 
In ubuntu 9.04 jaunty it doesn't work. ubuntu 9.04 is an upgrade from 8.10. As 
with the other users comments it was working fine in 8.10 which was an upgrade 
from 8.04.
I found a workaround, by stopping the graphical boot screen it seems to allow 
rc.local to start the software. I edited menu.lst:
title           Ubuntu 9.04, kernel 2.6.28-15-generic
root            (hd0,0)
kernel          /boot/vmlinuz-2.6.28-15-generic 
root=UUID=915a4563-e2ee-4842-999f-f4c55be09bf8 ro quiet splash
initrd          /boot/initrd.img-2.6.28-15-generic
quiet

quiet splash was deleted in the kernel line of this file, so everytime it boots 
the software starts now.
The thread of the problem is at:
http://ubuntuforums.org/showthread.php?t=1266614&page=2

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custom services do not start in auto after upgrade to 9.04
https://bugs.launchpad.net/bugs/372633
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