Thermal runaway on extruder hotend I am getting thermal runaway even after PID autotunning many times. I tried 10, 15, 20, 25 and 30 cycles and after reuploading FW onto the printer but I still get the error... 

I've built a copy of Prusa's i3 mk2 by following Building the cheapest possible Prusa i3 MK2. 

I have tried autotune with the cooling fan off, 50&nbsp;%, and 100&nbsp;%, but nothing changes.

The printer is in a closed cabinet room.

I was just watching it printing + temperature graph, and after ~20-30 minutes it starts jumping from 199.3-5 to 200.6-9... And that causes, after a few minutes, thermal runaway. The fan was on for 15 minutes or more. 

Any help?
If a temperature of (rounded) 201 °C is triggering TRP, then one of three things is the culprit:


The TRP Hysteresis is awfully trigger happy. See What is Thermal Runaway Protection?
Your Heater cartridge is not properly mounted and has a bad connection to the heater block and upon heating and expecting a much higher temperature but not measuring the associated increase it triggers TRP as it thinks "DANG! My thermosensor or heater cartridge must have fallen out of the heater block!"
Your Thermosensor has occasionally erroneous readings that are interpreted as temperatures way over or under 200 °C and trigger TRP.


To rule out the problems, do the following:


Check the mounting of the thermosensor and heater cartridge. Tighten if needed. The thermosensor should have no cracks (glass) or deformation (metal cylinder)!.
Check resistance and wiring of the heater cartridge (it should have some depending on the type) and thermosensor (If you use a thermocouple sensor, you might need to flip wiring).
Use a terminal with a graphic interface and look at the temperature output line as you heat up and print. If it has spikes or sudden valleys, you get occasionally erroneous readings and should go back to recheck your wiring or replace the thermosensor.
Only after making sure the physical side is ok, look at the TRP code and Thermal Settings in configuration_adv.h. Only alter these if you know what you are doing, as you do so at your own risk - the settings in the distribution are well proven to be safe, while alterations might turn TRP effectively off and turn your machine into a fire hazard. Which factors to increase carefully is detailed in this answer.