Why does the fluorescence signal drop sharply at the beginning of an artus® PCR run?
FAQ ID -1498

Air bubbles in the reaction solution may cause a strong fluorescence decrease at the beginning. In the Rotor-Gene® instrument those bubbles will be removed by the spinning action of the instrument. Insufficient mixing of sample and Rotor-Gene® artus® Master Mix may also lead to a steep initial fluorescence decrease due to an uneven distribution of the fluorescent dyes inside the tube.

As mentioned in the user manual, QIAGEN strongly recommends to thoroughly mix those two fractions (by pipetting up and down several times) prior to the PCR run.