A broadly observed phenomenon in experiments on molecular junctions is time dependent switching of the tunneling current. In many cases such behavior involves different current states which are attributed to the transfer of single atoms or functional groups in a molecule between different stable configurations. We describe here the investigation of the current switching observed in a molecular junction formed by a PTCDA molecule between an STM tip and an Ag(111) surface, which is believed to be due to the carboxylic oxygen atom switching between the surface and the tip. The switching process displays a strong dependence on the applied bias voltage between tip and surface, but a much weaker sensitivity to the bias polarity. We analyse the experimental data in terms of a minimal model Hamiltonian approach describing the coupling between an adsorbate level (a relevant PTCDA molecular orbital) to local vibrations excited by the tunneling electron. The switching rates as a function of the applied bias could be fitted with a physically reasonable parameter set.