jit.pwindow - no output when running as a standalone app

I am having trouble figuring out what is causing this.

I have a fairly sophisticated application which is drawing 3D shapes using jit.gl.mesh->jit.gl.render->jit.pwindow.

Whenever I run the application within Max, the jit.pwindow will show output 100% of the time. I have never seen it not show output. However, whenever I export this to a standalone application, I sometimes see no output in the jit.pwindow.

To make things even more interesting / frustrating - my app has a feature where you can pop out a window (jit.window), i.e., where I change the draw_to dest to the jit.window - and even if the jit.pwindow is not showing any output, the jit.window will always show output. This is done without ever stopping the qmetro clock.

This is a commercial app, so it will be difficult to share - but I am looking for pointers on how to debug jit.pwindow problems when running as a standalone. Anyone else ever encountered an issue like this?

One other thing to note - is that the qmetro clock does not start up automatically when the standalone is launched. There is a toggle button in the UI to turn the clock on/off.

So far, I have only tested this on Mac OS X - and always run as a 64 bit standalone app.

System Specs:
Mac Pro (2013)
Mac OS X 10.11.4
Max 7.2.2