Are you running on 10.9? Does App Nap take effect? Can you disable it?
In Unity, do you have run in background enabled? Are you scripting anything that touches the Syphon Textures / Materials ?
Ive never seen that behavior.
If you run Simple Client do you see your output, or do you see the server?
Are you running on a multi GPU setup?
Please give me concise details of your setup:
Machine, GPU, OS,
Syphon Plugin version?
Client app you are displaying?
Unity is Windowed and running a Server yes?
Does Simple Client and Simple Server exhibit similar behavior over the same time frames?