Update broke site, categories broken

Hi, we just updated to the latest version of the toolkit, Version 3.1.9, which took our site down. We are using i-transform theme. Once I’d seen the ‘major update’ notice after updating from IWP in the backend, I figured it was this plugin that broke the site. So I unchecked ‘use default i-transform slider’ from the page, which brought the site back.

Time for rebuild…as it lost the old slider completely. Thanks for that. Now, I cannot apply a category to anything either! It just unchecks. So I cannot re-add the slider, which is costing me time. What happened to break it so badly between version 2 and 3? Also I tried adding a new category. Now I have 4! 2 dupes appeared – none of which I can use. Or delete. Pretty bad! What’s going on??