Problem Resoled for real this time.
Something was getting pushed into the element that created the nivoslider. I added this line to line 12 of js\jquery.nivo.slider.js
$(element).children().remove('script');
I also saw that create_function was deprecated on line 760 of functions.php, I replaced that with this:
add_filter( 'loop_shop_columns', function($columns) {return 3;} );