The problem is due to that
[u]Autoscale X[/u] and [u]Autoscale Y[/u] of the drawingPanel "Simple_Pendulum" were set to  true as default.
Even the default range was -1 to 1.
But when the x,y is smaller than -1 , EJS will change the scale so that it will fit into the range automatically (because it was set to autoscale)

You can set the [u]Autoscale X[/u] and [u]Autoscale Y[/u] to[u] false[/u]. 
But you will need to change ymin and ymax to larger value , e.g. -1.5 to 1.5 or larger otherwise, it will be drawn outside the simulation region.

You do not need to set action to [u]_paly()[/u] in the texfield region. unless it was not running initially, and you want to start the simulation when user enter new value.

For those traces in the plotting panel, I would suggest you set [u]Max Points[/u] to a variable: e.g. maxpts
and define maxpts = 500(as integer) , then only the last 500 points will be shown in the trace.
Otherwise, the time scale will be changing all the time in the plottingPanel.