A recent investigation of an anomaly in the polarimetric measurements at JET is reported. A calculation, based on the Stokes vector and Mueller matrix method, has been developed to simulate the effects of the waveguide on the polarization of the propagating beams. These effects consist in rotations of the polarization and alterations of the ellipticity, and affect both the probing and the reference beams. The model which is assumed here is made up of a rotated retarder followed by a rotator, with three free parameters to be optimized. A very good agreement between the resulting calculated curves and the experimental calibration diagrams is obtained for the four vertical channels of the JET polarimeter. Variations of both phase shift and amplitude ratio are fitted by the model. This result supports the hypothesis that the waveguide system, which transfers the beams from the torus to the detectors, is the main source of the anomaly.