Assuming you're using the streaming server built into Windows Home Server (Windows Media Connect 2.0), it's told to activate and index the shares it's preconfigured to process. (It already has all required permissions, it's just not streaming.) It's
incapable of writing to the files or shares.
If you're using some other software, consult the documentation for that software; we can't help you...
I'm not on the WHS team, I just post a lot. :)