I guess you're talking about scope traces? Can you verify the scale factor of your scope traces?
Don't know about your software, but when scope traces go flat in Falstad's interactive simulator, it's because all values went to infinity for some reason as I was working. The simulator automatically scales the values to fit the finite space. This creates a teeny tiny scaling coefficient. It does not get corrected when normal values resume. Scope waveforms no longer appear.