I see 2 "Shop by" panels at a time.

If you see 2 shop by panels when using Improved Layered Navigation extension, it means one is default and othe other is added by the module.  In most themes the module removes the default panel automatically, but now it fails to do that because the panel has custom name. 

Please open the catalog.xml in your custom theme and remove all occurrences of the blocks with the template "catalog/layer/view.phtml".