Comment 2 for bug 220094

I had this problem for quite a long time now, actually I believe it does not compromise anything as long as you don't install or upgrade any kernel module needed at boot time. To answer your question, I don't know where update-initramfs reads informations from to know which initrd to update, but I solved the issue by calling:

update-initramfs -u -t -k `uname -r`

this way it replace any information about older initrd with the current one, so updating it every time the trigger is processed; I didn't try it yet, but I believe that you can simply add a new initrd trigger, without removing the formers, by calling update-initramfs without the "-t" option.