I have to admit I haven't done print and cut for a very long time so can't offer any help here but if you mean by the latest update you're using V4 it could be a problem with that. I have V4 on my laptop so I can get used to the layout as it's so different to V3 but haven't cut anything with it yet because my Cameo is used with my desktop pc which still has V 3 on it. When you say you can't get rid of some of the lines have you tried ungrouping or releasing the compound path on the the file then deleting what you don't want or if you have the Designer Edition you can use the eraser as it gives more choice than the eraser in the free version of Studio