Generally, I would think of update-initramfs not touching _all_ kernels rather 
a feature than a problem. For kernels that have not been touched (as the 
previous kernel demonstrates) this preserves integrity.
I am not sure I completely understand the upgrade progress here. There seems to 
be one step of udev being done before the kernel generates the initramfs 
(adding diverts?). Does this mean between that and the final configuration udev 
is in an undefined/bad state?
If that is true, maybe the solution could be to create a timestamp at the 
beginning of an installer run (if that does not already exist). The kernel 
always runs update-initramfs with the version number, so I assume udev runs it 
without a specific version and that triggers the default. This default would be 
changed to initrd files that have been modified since the installer started if 
the timestamp file is there.
Steve, how does this sound to you?

-- 
boots into busybox with 2.6.28-11-generic kernel.
https://bugs.launchpad.net/bugs/364029
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