What RR does is:
1-Find the window of your app to embed, if not found: do nothing
2-Checks if the window is in the right size/position, if it is: do nothing
3-Adjusts the size/position of the embedded app to match the defined in the skin
The above is done about every second - If your other application is doing anything to the embedded app, this could be why you see it flashing. I know Mitch also added some advanced options for embedding apps so this could also have an effect on it for the better or worse.