It's a littl hard to know what's going on without seeing your project. If you can post a screenshot of your comp and timeline it would help in understanding.
Generally speaking, Shatter should be applied to 2D layers, not 3D layers, to work properly. So in your case, you should scale and rotate your 3D image, then precompose it using the "Move all attributes into new composition" function.
This means you'll now have a 2D precomposed layer in your main composition, and it should be the same size as your comp. Apply Shatter to this layer. If you are using a 3D camera in your main comp, set the Camera System selector in Shatter to "Comp Camera".
You can continue to change scale and rotation of your original 3D layer inside the precomp.
To animate the start time of the Shatter effect, use keyframes to change the "Radius" setting within Force 1 and Force 2. So long as the Raius value stays at 0, nothing will Shatter. As soon as you increase the Radius setting above 0, the Shatter effect will begin to execute. So, typically, you'll move along the timeline to the point you want Shatter to begin. Set a keyframe for Force 1 Radius to 0. Move forward another frame or 2, then set another keyframe to your preferred radius setting (typically a decimal below 1.0).
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