"some areas of the fence seem extremely hot, while others don't seem to be working, even on the same unbroken line". So current in a section of fence is not working but is on opposite ends of that section? I don't know what you are using for insulators but I have had on rare occasions instances where the wire actually wore through the insulator and was in contact with the nail that was holding it in place. It was grounding out on the nail but on visual inspection looked perfectly fine. Could this be your problem?