In an ideal world, chkdsk.exe will fix all errors. In the practical world
it ignores some errors. However, your problem may lie elsewhere.
I suspect your path is too long. Under Win2000, the combined path
& folder length cannot exceed about 250 chars. However, if you have
a share like so:
net share Data="d:\User Data\Finance\Financial Year 2002-2003\Budget"
then you have consumed 52 chars. By linking a drive letter to this share:
net use x: \\YourServer\Data
your users can create a 250 char structure on drive X:, which clearly
exceeds the maximum path length for drive D:. This would cause problems
when backing up files or copying them.
You can easily prove this by issuing the "net share" command on the
server, then running cacls.exe against the shared drive. Your error might
disappear.