Game client settings not saving per instance (Solved)
Go to your "My Documents" and find a folder called "Diablo III". In that folder you should see a file name D3Prefs.txt. Make as many copies as you need.
In my case I have:
D3Prefs-1.txt
D3Prefs-2.txt
D3Prefs-3.txt
D3Prefs-4.txt
along with the original in the folder.
Now go into ISboxer and right click on "Virtual Files" in the top left pane. Select New Virtual file and rename it to D3Prefs.txt.
Left Click on the new virtual file you just created then drag each Character from the top left pane into the virtual file just like you did for the setup to get multiple copies of D3 to run.
Then click into each character in the bottom left pane in the Virtual file setting and set "Virtualize as" to the names of the files you copied earlier.
For example I have
jsigley1 virtualized as "D3Prefs-1.txt"
jisgley2 virtualized as "D3Prefs02.txt"
and so on...
I left the original file unused in this and just made new copies of each for each character. This way when you run the game just from the desktop without Innerspace it will use the original file and not affect or be affected by settings changes to your Innerspace ran clients.
Hope this helps someone.