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When you shut down or reboot, the scripts referenced by the symlinks in /etc/rc.d/rc6.d are processed. On my box (also Mandrake, and also running Samba), one of those links (K35smb; the "K" means Kill) runs /etc/init.d/smb, which starts or, in the case of a shutdown/reboot, kills smbd and nmbd, as far as I can tell.
I think the initial "switching to runlevel 6" message comes from init, but from the information you've given, epecially regarding the Samba corruption, you might want to look at the scripts that get executed at shutdown/reboot and see if there isn't something amiss there. Sorry I can't offer anything more specific, but I haven't enountered this particular problem before and I'm still more than a bit of a Newbie.
ive noticed since i reinstalled samba that the problem stopped... so maybe there was a file corruption...im not sure... i really have no clue as to hoe the runlevels work... i am so used to windows in that there seems to be only one run level...im sure, oif course, theres more but windows tens to try to keep underground things from becoming apparent to the user...
If you think Windows tries to hide its inner workings from you, check out a Mac- it hides everything from you.
As far as runlevels go, Windows actually does have a few equivalents. When you boot into "safe mode" or "command prompt" in Win, it isn't the same as booting straight into the GUI (Windows). Less services are started, and fewer drivers are loaded.
The comments at the beginning of /etc/inittab describe the different runlevels in Linux a bit:
[# 0 - halt (Do NOT set initdefault to this)
# 1 - Single user mode
# 2 - Multiuser, without NFS (The same as 3, if you do not have networking)
# 3 - Full multiuser mode
# 4 - unused
# 5 - X11
# 6 - reboot (Do NOT set initdefault to this)
The above runlevels apply to Redhat and Mandrake at least, but some distros (Slackware is one) use a slightly different numbering scheme.