You measure the temperature at the still head just as everyone has said.. your thermal rearrangement is likely done by the time you hit 260C, you could just distill under vacuum?
The reason why the temperature of the liquid is higher is due to the distillation being a non-equilibrium process (and a high difference in Gibb's energy, or mixture fugacity of the components, or of chemical potential of the components -- three things saying the same thing) is required to give enough kinetic energy for the process to be run at an appreciable speed. Basically, the liquid has to be super-heated...
The other explanation, less mathematical/theoretical, is that the liquid is probably contaminated by miscible, non-volatile components.