Home Folders Not being Created Correctly

I'm having some sort of major issue with my directory and/or afp setup.
I'm trying to create new users and the home folder won't be created at all. If I change the permissions (give write access to the user's group) on the root of the share that hosts the home folders it will create one but it is mangled. The home folder only conatins a Library and Desktop Folder. Documents, Movies, Music, Pictures, Public, and Sites are missing. Also the permissions on this newly created home are mangled being 700 instead of 755.
All Existing Users are functioning okay but creating new home folders is broken. It has been a while since I've needed to create new users. I'm worried it may be hard to isolate the cause and effect. I have done software updates 10.4.6 and now 10.4.7. Also I changed this machine to handle local DNS.
Any Ideas?
XServe G4 1.0 Single 500GB Mirrored RAID on Internal Drives 10.4.7 Server

We also have this problem, and before I go and re-edit the home folder entries for each of our 600-odd users, I'd appreciate if you could confirm that this solution is going to work for me...
Troubleshooting another problem, we applied the x.4.6 update about the same time as the Network Mounts were turned off then a restart and turned back on again. A bad combination.
Faced with a Monday morning "None of the students can log in" crisis ("you are unable to log in to the user account "username" at this time..."), and thinking that the problem had been caused by my turning the network mounts off, I discovered that student mount points now show (in WM's Home tab) as "afp://10.224.96.2/Students" where they used to be "afp://mainserver.westlandhigh.school.nz/Students".
The easy fix to the problem (not knowing about artnum 303697 at that point) was to reassign the home folders to the 10.224.96.2 home. (when you don't know what to do, you do what you know how to do). This got the users happily working again, although there were all sorts of strange problems relating to disk quotas that some users had to work through.
a few days later the log entries about DNS were noted, artnum 303697 applied, and changeip fixed those things. hostname responds correctly as mainserver.westlandhigh.school.nz. Everything ran reasonably well for the next couple of months, although the AFP/CPU hogging problem mysteriously appeared...
x.4.7 seems to have solved the AFP/CPU hogging, but now we've discovered a problem creating home folders for new users.
Tim's fix on 3rd August shed some light... An interesting quirk of using Presets is that we still have a Student preset that puts the FQDN name in the home folders list. So we can leave the FQDN home folder selected, click Create Home Now, and on Save, the folder is created. But the student can't login: "you are unable to log in to..."
Change the mount point to the IP number, Save, and it almost works - the system tells the user they are already logged in to another computer... Selecting Allow simultaneous login from Advanced solves this problem, but leaves the system open for the student to attempt to log in twice, with the potential for havoc there. It's also not a wonderful work around as the other staff who sometimes enter new users are likely to miss one or more of the extra steps...
I guess that I'm going to have to turn Network Mounts off in Sharing, and then turn them on again to get the right set of mount points showing in Accounts/Home, and then work my way back through all the students and point them back to the FQDN mountpoint again?
Is it likely to be worth the pain? Will it cause some other problem to arise? Is there an easier way?
G4 DP 1.25 Mac OS X (10.4.7)
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