For anyone having this same issue, you can roll back to a pre-3.0 version here: https://plugins.svn.wordpress.org/custom-sidebars/tags/
I am experiencing the same issue. I tried updating the RTL css from one of the other forums but it did not change anything. The v.3.0 Custom Sidebars completely disrupts the widgets section of wordpress and I can not edit widgets/sidebars when it is activated. I have many client websites using this plugin and now all of their sidebars have been wiped and customization functionality is impossible after updating to 3.0. Please please please fix this issue and send out an update.
