Shape layers are a very special case in After Effects.
They're like an object based model inside of AE's layer based model. This means that, just as in Adobe Illustrator for instance, you can create multiple objects inside of a shape layer, and edit or animate its' attributes independently.
Every time you drag with a shape tool in a shape layer, you create a new shape group in that shape layer.
A shape group has its' own transform properties (position, scale, rotation, anchor point, opacity).
So, as you see, you can have the layer's transform properties (like any other AE layer), and also have each group's transform properties (only for shape layers).
That invisible box you're seeing is most likely the bounding box you get when you select a shape group inside a shape layer, rather than selecting the whole layer.
Motion Sketch only works with the top level position property for the whole layer, not with the position properties inside the shape groups.
I think what you want in this specific case is to center the anchor point for the whole shape layer before using Motion Sketch, using the Pan Behind tool. This is because shape layer content is usually created so that each group's anchr point is centered, not necesarilly the layer's anchor point. Normally, that's a great thing. But not so much if you want to use Motion Sketch, for instance. Your content may not thread as you expect in the motion path if you don't adjust the anchor point for the whole layer.
Does this help?
Thanks for your response. I'm not sure if I am understand you.
I am only trying to animate 1 simple shape (which is the only in the animation), so there is no grouping involved. The center point is in the right place.
After I hit "Start Capture" in the Motion Sketch panel and go to drag the shape---an outline of a box comes out from the pasteboard (is that what you call outside the work area in AE?) It starts to capture the motion based on this box.
The box is not in the same place as the object, it comes from outside the wrok area.
If you post a screenshot or the project itself (remember to change the .aep extension to .txt so the forum system can take it), it will be easy to see what's going on. I suspect it's related to what I posted before. Even if you use a single group, there's still a group with a different anchor point from the layer's anchor point.
Shape layers use a different coordinate system model based on the center of the layer, not the top left corner. This may have some bad influence. In addition, shape layers being a parametric vector rasterizer, you always move the whole layer, not anobject inside your group. Basically a shape layer always has the size of the whole comp, even if your content may only cover a fraction of the area. This affects of course how the bounding box is being displayed during motion sketching or moving stuff around with wireframe interactions....
You can also try to pre-compose your layer shape and apply the motion sketch on the precomp. (ctrl-shift-c / cmd-shift-c to precompose the selected layer(s))
So I finally got it to work. It something to do with the 'wireframe' optio, and Yes I did have to use the Pan behind tool.
Thanks all for your help and responses!!!