Footer Editor Removing Java script tags

Hello Sakin, Thanks for a great product and great support. I am running a subfolder multisite. I have had an issue with a particular plugin since updating to WP 3.7.1. The plugin works fine on the pages associated with the subfolder sites, however, after updating to 3.7.1 the plugin disappeared from the pages associated with the main site. I tried the standard uninstall/install the plugin, deactivated all the other plugins, etc. Same problem. Checking the source code showed there was no code for this plugin on the main site pages, but there was code on the subfolder sites' pages. The plugin support team suggested I copy the java script code directly into the footer. I did that in the footer editor under theme options, but when checking the footer all I saw was code. I checked the source code again and noticed the opening and closing script tags had been removed. I went back to the footer editor, and sure enough the editor had automatically removed the script tags but left the rest of the code. I tried repasting the code into the footer editor with the same result (i.e., removal of the opening and closing script tags). My url is attorneymott.com however it is not live. Please email me and I will set up a user account for you if you need to take a look. I would prefer that the plugin just work without having to paste code into the footer, but I understand that problem may not be due to the theme. If there is a solution other than pasting the code in the footer that would be great. If not, I guess I need to figure out why the footer editor seems to be erasing the script tags. Thanks for responding at your convenience. JM