I would need to see your input signal file and your simulation setup, but I best guess would be to look at the 'simulation frequency' in setup. Typically in harmonic simulations, the time step is set based on the lowest wavelength in the materials. It is possible that this is calculated by looking at each material's speed of sound and dividing it by the frequency (set in setup).
Can you maybe try changing this frequency to a higher one (maybe one representative of your input wave form) and see if that fixes your problem? Either way, let me know so I can take a look at the code and make a fix for this in the future. Alternatively, in user defined sources, is there no option for sampling frequency (1/timestep)? That would then be your fix - set the sampling frequency / time step to something that can resolve your waveform.