I can't tell without seeing your system, but I suspect that you're actually operating inside an initramfs RAMdisk. It populates the RAMdisk from file when it loads, then otherwise ignores it. To get things added to that, you need to update that file.
here is as much information as I have on initrd. Be careful when working with yours, you could easily make a system unbootable by building it wrong or not having the correct permissions on things.