Temperature is not as simple thing as one would assume. The higher the temperature is, the more violent things occur. Heat is conducted on parts, heat is radiated from one place to another, and heat is convected with the gases. This mean there is no uniform temperature inside the furnace or inside the sample holder. Instead there are changing forces and if the conditions do not change, there may be some equilibrium.

Temperature can be measured with the thermocouple of the furnace itself, but also with thermocouples inside the sample holder. In most cases they will not indicate the same temperature for simple reason; the thermocouples are not experiencing the same temperature. This is not a problem, but may be confusing for people who have not dealt with high temperature furnaces before.

The chamber inside a furnace has a gradient of temperature. Some furnaces have less, some have more. Here is an example of a typical gradient.

When the furnace chamber has a sample holder in it, things change a bit. Reading temperature from a thermocouple inside a sample holder, the result will depend on the sample holder location in the furnace but also on many other things. 

If the furnace controller is guided by a thermocouple that is located inside the sample holder, there are important aspects to consider:

1. Safety. If the sample holder is not inside the furnace, and the furnace does not include guard system to protect from overheating, the furnace may end up melting it's heating elements.
   
   
2. Delay. Heat takes time to penetrate from the furnace heating elements all the way to the thermocouple tip inside the sample holder (There are dense walls to penetrate). This effect is particularly strong at low temperatures (below 400ºC). The controller does not understand this and will try to heat more and more. This will cause the system eventually to heat more than what was required, and then correct for that overheating by under-heating and so on. It meant the temperature may oscillate around the target setpoint for quite a while. To overcome this problem one must use the controllers feature called ramp rate, with very slow ramp (for example 1 degree per minute), or optimize the controllers PID settings for this specific case.