The module-init-tools upstream maintainers decided that in the future the files in
/etc/modprobe.d/ will be processed only if they have a
.conf suffix. The latest module-init-tool release complains loudly for each one and still processes them, but this will change.
Please update your packages and remember that the files in this directory are opened and parsed every time modprobe is run (and it is run very often at boot time!), so try to look at the big picture and install a file there only if it is really needed. Do not install a file if it only contains comments, if it is only useful for some unusual environment or if it not needed by the kernel currently in the archive (nowadays most drivers have their own aliases built in, check
/lib/modules/$KVER/modules.alias and submit a kernel patch if they are missing).