How do I model a simple metastable flip-flop in ngspice?
Setting arbitrary initial conditions isn't really "allowed," in that there's no realistic way that the circuit could ever get into that state. The sudden change between that takes place when the initial condition is removed from the circuit does not play well with simulators, as you have seen here. You could probably reproduce similar behavior using ideal switches.

You may want to try simulating with initial conditions around where you see the flat areas in your simulations, maybe around 0.5V or 0.9V, so there is not such a sudden change when the initial condition goes away.