Alright, after a bit of investigation on the Bethesda forums I've found a couple of user-made fixes for the problems introduced by the new patch.
The resistances bug is fixed by the latest version of SKSE: http://forums.bethsoft.com/index.ph.....extender-skse/
The 360 controller bug is fixed by an edit to the controlmap.txt file by a forum member named repeater: http://forums.bethsoft.com/index.ph.....#entry19561742

Now I just need a fix to make bookshelves work again and it'll all be good as new!