I have not found the reason, but I have the solution I think. I am not sure if other functionality is needed from the tools package other than the tooltips on the contact forms. Is there? I found that if you only include the code for the tool tips, the conflict goes away.
On the jquery toolkit download page, you can select a download that only consists of the tooltips. I then modified the custom-contact-forms-front.php file to wp_enqueue_script(…/jquery.tooltip.min.js’); instead of the jquery.tools.min.js file.
(I had the issues with colorbox and superfish menu)
