The motional stark effect (MSE) is an effective method to assess the rotational transform in magnetic confined plasmas by measuring the polarisation angle of the emitted light. It relies on the Stark-splitting of the Balmer alpha emission, caused by the interaction between the injection of neutral beams and the background plasma. A prototype MSE diagnostic system, which relies on spectrum measurements taken using different linear polarising filters, has been installed on the Wendelstein 7-X stellarator (W7-X), and its diagnostic capabilities have been demonstrated. In this work we present an upgraded MSE diagnostic system and discuss the comparison between the experimental data and the forward model originally developed for the beam emission spectroscopy measurements at W7-X and modified to include the polarising optical elements. The experimental data and the model results show a good agreement for relative changes of the polarisation angle for different plasma . However, the evolution of the polarisation angle during electron cyclotron current drive experiments could not yet be resolved due to limited signal-to-noise ratio. Possible upgrades to improve diagnostic performance are outlined.