I have experimented the same issue with almost every project, in my case the issue trigger is the realTime Shadows, when I turn off the shadows, the warning is not shown.
The fact that the only way to see the warning is running the project in the editor, doesn't mean that the problem will disappear when the application runs on device, in fact a very notable drop in performance running on device is evident when the warning is shown in the editor, well, finally this is the reason for these warnings, is in't ?
The problem persists in the new 2.8.9 vuforia version unity extension in Unity 4.3.4f1 Standard
The warning is pretty clear:
Tiled GPU perf. warning: RenderTexture color surface (0x0) was not cleared/discarded, doing <run with profiler for info>
It is a buffer that is not cleared or discarted, in the following demo project I have reproduced the issue, it's a very simple project with just 2 meshes and one directional light, using the chips&stones marker.
If you run the project on the editor with hard light's shadows active, you can see the warning, if you turn off the shadows the message no longer appears.
The link to download the project:
Thanks a lot for your help