This paper aims to address two intrinsic phenomena encountered in mobile manipulator robots, but often neglected, with the objective of improving the overall accuracy of end-effector pose estimation. Firstly, after performing stateof-the-art geometric calibration of the arm, we propose two identifiable mathematical models to account for non-geometric effects: a model for the mobile base suspension system and a model of non-linear inaccuracies of joint angles estimates. The latter is due to backlash and misaligned encoders mounting. Then, the proposed models were experimentally validated on the mobile manipulator TIAGo using a stereophotogrammetric system. Overall, the end-effector pose accuracy was improved by 60% when compared to the nominal manufacturer model, with root mean square errors (RMSE) of 5.7mm and 2.7deg for positional and orientational errors, respectively.