Hi Damian,
You will have to figure out what part of the JS is causing the tabs to behave incorrectly and then figure out a way to modify the script so it doesn't cause problems.
You could also remove the JS include lines from your layout.master, place them in a separate HTML file and upload the HTML file to\Data\Sites\[sitenumber]\htmlfragments and then use the "HTML Fragment Include" module to include on the page with the SlideShow.
Hope this helps,
Joe D.