It turns out this is well hidden, but I think I have nailed it (but cannot check).
The file /usr/share/msec/security.sh governs the daily security check (there is another file for the hourly check). I think the area to modify starts at line 74:
CODE
# Modified filters coming from debian security scripts.
# rootfs is not listed among excluded types, because
# / is mounted twice, and filtering it would mess with excluded dir list
TYPE_FILTER='(devpts|sysfs|usbfs|tmpfs|binfmt_misc|auto|proc|msdos|fat|vfat|iso9660|ncpfs|
smbfs|hfs|nfs|afs|coda)'
MOUNTPOINT_FILTER='^\/mnt'
DIR=`awk '$3 !~ /'$TYPE_FILTER'/ && $2 !~ /'$MOUNTPOINT_FILTER'/ \
{print $2}' /proc/mounts | uniq`
PRINT="%h/%f\n"
EXCLUDEDIR=`awk '$3 ~ /'$TYPE_FILTER'/ || $2 ~ /'$MOUNTPOINT_FILTER'/ \
{print $2}' /proc/mounts | uniq`
export EXCLUDEDIR
My understanding is that this excludes a list of mounts from scanning, provided they match on the filesystem (line 77, starting with TYPE_FILTER and isolated in above listing; note it excludes smbfs, but doesn't exclude cifs) AND/OR mount-point (/mnt) -- (Somebody who knows awk pls step in to confirm this). Your setup matches neither, so is included for scanning.
I suggest you add
|cifs to line 77 (inside the quotes) and test again; if it still fails then ensure your share is mounted in /mnt and try again. If it still fails then I am wrong.