As I was hit by this problem recently, I'm glad to see that upstream 
initramfs-tools 0.90 adds a configuration setting to have 'update-initramfs -u' 
regenerate all initrds. The configuration variable 'update_initramfs' in 
'update-initramfs.conf' could already be used in versions prior to 0.90 to 
disable 'update-initramfs -u' at all. Now it can also be set to 'all'. 
See 
http://git.debian.org/?p=kernel/initramfs-tools.git;a=blob;f=debian/changelog;hb=8b4b8b0ced679130f768cb10df8f78c1bb513281

It's not in hardy, but it should work in intrepid, which currently uses
initramfs-tools 0.92.

-- 
update-initramfs should update all initrds
https://bugs.launchpad.net/bugs/45225
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