Check that you haven't got a resistance between the hot end and the thermistor somehow. Shorts are bad, but a high resistance (say 10K-10Mohm) is even harder to debug. Unfortunately many glues suitable for use on hot ends can be somewhat conductive. Where possible, avoid applying any to pins on either the hot end heater (eg: resistor leads, etc) or the thermistor leads.
The thermistor is (usually) anything up to 100Kohm at low temperatures. If you have any resistance between the hot end (which is 12V normally unless you're running a higher supply) and the thermistor, this will feed into your thermistor signal line, skewing the temps. If that voltage on the thermistor signal line gets too high, you can actually damage your electronics (most don't have over-voltage protection on the thermistor pins).
The thermistor is (usually) anything up to 100Kohm at low temperatures. If you have any resistance between the hot end (which is 12V normally unless you're running a higher supply) and the thermistor, this will feed into your thermistor signal line, skewing the temps. If that voltage on the thermistor signal line gets too high, you can actually damage your electronics (most don't have over-voltage protection on the thermistor pins).