I just went through all this with Windows 2000 Server but I didn't have the disappearing files.
My problem was I wanted long file name support but that isn't included with Macintosh Services on Windows 2000. I could either mount my share with AFP and have icons, etc or mount the share with SMB and have long file names but also loose the ability to use special characters in the file names.
What I noticed was when I would switch the way I mounted either by SMB or AFP I would loose resource forks. As long as I stayed with on or the other then my resource forks would stay intact.
What I ended up doing was running Dave on my 10.2.4 box so I could use special characters in the file names. I can do this because Dave recognizes if your mount point is a NTFS volume. This might not be the case of NT, I don't remember if NTFS was around then. Oh yea, I did search all over the net to try to find a way to configure the Samba Client to recognize a NTFS mount but I couldn't find anything. I'm not sure if it's Apple that limits the SMB sharing to the FAT32 file formats or if it's Samba. I'm sure someone with more experience then I could elaborate more on this.
Download Dave and give it a try, they have a free demo. It does get expensive if you have a few machines but for only one or two it might do the trick.
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Hope this helps,
Brad