Odd… really should be working because I’m running Widgetkit 1.4.6 on WP 3.6.1 as well. Shouldn’t matter really what theme either. So everything was fine before you updated to WP 3.6.1 then it went crazy? Is it possible to contact me with a login for your admin? If so, is it ok also if I create a couple slides or at least a new slideshow with some sample images to test?
So far even with my local test site, I have not experienced any issues. However, if for some reason Widgetkit still is not working 100%, it’s optional for the theme which means you can always try other plugins, and yes, if you decided to try the LayerSlider, you could do that, but does come with a slight learning curve. But also note that this one is also optional but it is a paid $15 plugin. Of course, you still have a lot of other sliders you can try that are free too.