Now I will remember how to get rid of these message. First, verify that your running kernel and the /usr/src/linux are OK:

$ uname -r
2.6.12-25mdksmp

$ ls -l /usr/src/
lrwxrwxrwx 1 root root 18 sep 21 11:20 linux -> linux-2.6.12-25mdk/
drwxr-xr-x 21 root root 4096 aoû 30 12:24 linux-2.6.12-24mdk/
drwxr-xr-x 21 root root 4096 sep 21 11:32 linux-2.6.12-25mdk/

The important part is "2.6.12-25mdk" (If not, update, and install same kernel and kernel-source)

$ cp /boot/config-2.6.12-25mdksmp /usr/src/linux/.config
edit the Makefile, remove the "custom" in extraversion and put instead "smp" if needed

$ make prepare

(edit: add this too if it complain about modpost) $ make script

And, Voila, your kernel tree is OK