The dynamics of a molecular junction consisting of a PTCDA molecule between the tip of a scanning tunneling microscope and a Ag(111) surface have been investigated experimentally and theoretically. Repeated switching of a PTCDA molecule between two conductance states is studied by low-temperature scanning tunneling microscopy for the first time and is found to be dependent on the tip-substrate distance and the applied bias. Using a minimal model Hamiltonian approach combined with density-functional calculations, the switching is shown to be related to the scattering of electrons tunneling through the junction, which progressively excite the relevant chemical bond. Depending on the direction in which the molecule switches, different molecular orbitals are shown to dominate the transport and thus the vibrational heating process. This in turn can dramatically affect the switching rate, leading to nonmonotonic behavior with respect to bias under certain conditions. In this work, rather than simply assuming the density of states to be constant as in previous works, it was modeled by Lorentzians. This allows for the successful description of this nonmonotonic behavior of the switching rate, thus demonstrating the importance of modeling the density of states realistically.