I've done a lot of digging around and believe that this might be a bug.
/sbin-modules-update
Starting at line
143
143 for x in ${CFGFILES} ; do
144 [[ -r ${x} ]] || continue
145
146 if [[ $(sed -ne 1p "${x}") != "${HEADER}" ]] ; then
147 ewarn "Warning: the current ${x} has not been automatica lly generated"
I think I seen a previous BUG report where the expected header of the file was not found. /etc/modules.devfs
-rw-r--r-- 1 root root 3516 Feb 19 2006 modules.devfs
I'm not sure how to decipher the expression

RTFM time.
[EDIT]sys-apps/baselayout-1.12.4-r7 has just been release - The error persists[/EDIT]