I don't believe the subst is broken in Win9x, rather its functionality was extended in WinNT & higher. In fact, I believe it was extended in NT to specifically help overcome NT's inability to map deep shares.
Jens is right though. With Win9x clients you must create individual hidden shares. There is no way around this. The NT user manager does not actually automatically create shares, they are sort like pseudo-shares.
Another point, I don't believe NT servers can make these pseudo-shares invisible to other users. I not really familar with all the intracies of Win2000, maybe it can do it.
Finally, if I am reading you right you are planning to move these pseudo shares to a non-NT machines. I am not sure you can do this and maintain functionality. I though the dual concept of ownership & shares was a microsoft specific construct. Have you tested this for NT clients?
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Jack