Hi @hyde014,
I have tested on my test site using latest version of Custom Sidebars plugin and found it's working fine.
When I press the Sidebar Location selection button when in WIDGETS the whole lightbox window never undims/loads properly. I just get the spinning load wheel indefinitely.
Can you check the javascript console for errors?
Find information about how to open JavaScript browser console :
http://webmasters.stackexchange.com/questions/8525/how-to-open-the-javascript-console-in-different-browsers
http://codex.wordpress.org/Using_Your_Browser_to_Diagnose_JavaScript_Errors
Let me know what errors if any you are getting when clicking on Sidebar Location.
You can just try on your development site using default WordPress theme like Twenty Thirteen and deactivating all other plugins as displayed in the following flowchart to know which theme/plugin is conflicting if any.
http://premium.wpmudev.org/wp-content/uploads/2013/12/Support-Process-Support-Process.png
Secondly any reason why my sidebars show up different now even though I'm using the same widget boxes provided by my theme?
See Page for normal sidebar: http://www.amish365.com/
See Page for custom sidebar: http://www.amish365.com/amish365-marketplace/
This may be a theme specific issue. To confirm could you please try temporary using default WordPress theme like Twenty Thirteen and check whether both the sidebars are displaying fine or not.
Kind Regards,
WPMU DEV