About 1 out of 5 times i'll get into windows and the network shared drive will actually show files. It's showing empty past the second level of directory.  On another note it's duplicating my downloads and media directories. Not the data just downloading the directory which is odd. I can live with that but through windows I can't see anything in the files a lot of the time. Does this have to do with disk spindown? Is there something I should do to make it better? Anything I could put on cache to let it know where the files are located faster?

There is the Dynamix Cache Dir plugin that is intended to help in these situations.  I have it installed and it seems to work on my media stores (~ 2500 items).   Be careful as to how many items you are caching because it caches the info in RAM and it can get 'bumped' if the system needs more RAM for another task.  (Next time, you go to use it, it has to rebuilt everything...)

One more thing, make sure that you have Windows Explorer set up so that it only displays file names.  Displaying things like thumbnails take a long time to load across a network.

 

You can right click on the mapped drive, select 'Properties', Select 'Customize',  Then from 'Optimize this folder for:' pick 'General items' from the dropdown list, and apply to all subfolders.