Disaster Both Before and After Theme Upgrade

Hi, I created a website for a client using CatchBox (free version), which launched a couple of weeks ago. He sent me a text yesterday noting that his home page had somehow rearranged itself and that the content of the page now took up the entire top section, with the sidebar widgets now below that content, even though the default layout was selected and was set to "content on the left." I looked at a copy of his site on my test server, and noticed an update was available for Catch Box, but unfortunately the update made things even worse. Now a "skip to content" message appears above the header image, there is NO padding around the header image, and an additional menu appears below the embedded primary menu. I have looked at all settings and they are set up correctly, yet this is the result. Any ideas how to fix the original problem OR the new problems associated with the upgrade? I can simply tell him not to upgrade to make sure he avoids them until they are corrected, but there exists the possibility that he might "forget." I have screen shots if you would like to see them. Thanks, E. Marie Robertson