update-modules merge ALL files in /etc/modules.d, including the backup ones. For example, if you edit /etc/modules.d/EXAMPLE with emacs, you have /etc/modules.d/EXAMPLE and /etc/modules.d/EXAMPLE~, and update-modules will merge both.
Created attachment 5042 [details, diff] Patch to fix this problem This patch fixes the bug
Fixed on CVS, thanks.