I have not experienced these Annotate Dot issues when using version 5.1 (5B161) but am encountering the following if using version 5.2 WIP (5C146w) running OS X El Capitan v10.11.4:
Unable to change the layer of the Annotate Dot after placement from within the Object panel under “Basic” info in the Right Sidebar. For example, if it’s on Layer01 but I want to move it to Layer02, one can select Layer02 from the drop down menu; however, the object properties of the Annotate Dot remain on Layer01. As a temporary workaround, I right click on another layer in the Layers panel & select “Move objects to this layer” so the Annotate Dot is assigned to a different layer.
The Annotate Dot text does not update after editing & neither will the font style or size.