warning after update to wp 3.5

The SQL queries are not property prepared in the current version. Update category_icons_php with this file I bug-fixed: https://docs.google.com/open?id=0B7JEImS_HANHVlRzNnJrb3E2QVU

Above solution removes the warning… I must then re-select the icons for each category (OK, I can do that). Upon selecting the icons they show up on the page, but upon saving (clicking “Select Icons” at the bottom of the Select Category Icons page), they don’t show up, and instead display broken links on the Select Category Icons page (broken links appear to point to
“https://www.sitename.com/wp-content/uploads//”
instead of
“https://www.sitename.com/wp-content/uploads//image_name.jpg”
Please advise…

Did you upgrade to WP 3.5.1 ?