The time domain stability of microwave spin torque oscillators (STOs) has been investigated by systematic micromagnetic simulations. A model based on internal spin wave reflection at grain boundaries with reduced exchange coupling was implemented and used to study the oscillator under quasi-stable operating conditions. Telegraphic mode jumping between two operating frequencies (23.3 and 24.1 GHz) was observed in the time domain with characteristic dwell times in the range of 10-100 ns. The oscillating volume was shown to have a different shape at the distinct operating frequencies. The shape difference is governed by spin wave reflections at the grain boundaries. The resulting non-linear behavior of the oscillator was shown to be a collective effect of spin wave scattering at different locations within a few spin wavelengths from the nano-contact.