Systems and methods of registration system control are provided that compensate for differences in physical properties of various substrates being transported through the system that impact the displacement of the substrate through a given path. Exemplary systems of the invention include at least one roll pair formed by a first, driven roll and a second roll defining a nip therebetween that is part of the transport path through which a substrate is passed. A prestored lookup table includes empirically- or theoretically-derived compensation factors for plural different kinds of substrates, with each compensation factor being based on physical characteristics of the substrate that impact actual travel length of the substrate along the transport path, such as the substrate's mass per unit area, which has been found to have a strong correlation with a substrate's bending stiffness, which has been found to have a strong correlation with detected deviations in linear travel path. Upon input or determination of the substrate being registered, the system adjusts the drive profile of the drive roll by the compensation factor. This is preferably by adding the derived paper path length adjusting value to the actual nominal length between the drive roll pair and a desired registration position to take into account an arcuate or non-linear travel path due to flexure of the substrate. A suitable compensation factor compensates for the amount of angular rotation of the drive roll so that the travel path length of the substrate is appropriated compensated.