We investigate the origin of the experimentally observed varying current-frequency nonlinearity of the propagating spin wave mode in nano-contact spin torque oscillators. Nominally identical devices with 100 nm diameter are characterized by electrical microwave measurements and show large variation in the generated frequency as a function of drive current. This quantitative and qualitative device-to-device variation is described in terms of continuous and discontinuous nonlinear transitions between linear current intervals. The thin film grain microstructure in our samples is determined using atomic force and scanning electron microscopy to be on the scale of 30 nm. Micromagnetic simulations show that the reflection of spin waves against the grain boundaries results in standing wave resonance configurations. For a simulated device with a single artificial grain, the frequency increases linearly with the drive current until the decreased wavelength eventually forces another spin wave anti-node to be formed. This transition results in a discontinuous step in the frequency versus current relation. Simulations of complete, randomly generated grain microstructures additionally shows continuous nonlinearity and a resulting device-to-device variation in frequency that is similar to the experimental levels. The impact of temperature from 4 K to 300 K on the resonance mode-transition nonlinearity and frequency noise is investigated using simulations and it is found that the peak levels of the spectral linewidth as a function of drive current agrees quantitatively with typical levels found in experiments at room temperature.