Wow! Knob and Tube! Brings back horrible memories! You mentioned that the two wires coming from the bottom of the box are hot. Did you disconnect them from the switch to read them. If it's a three way, the hot wire will feed one leg of the switch in one position, and the other leg of the switch in the other. The hot is typically attached to the odd colored terminal of the switch. Given your house is really old! (knob and tube), you could have a switch covered over somewhere that feeds the light in question. You should try to determine where this is, and eliminate it, by tying the light back to the controlling switch.
If the switch were switching a neutral then it would have to be double pole, double throw, not a three way.
Good luck with your old house, and be careful for asbestos while changing things or working in crawl spaces. Breathing is important!