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I ended up implementing my own subclass of AbstractXYAnnotation which translates but does not scale the Shape to solve problem #2. This also fixes problem #1 because the call to java2DToValue() is now made within the annotation's draw() method, not before the chart component has been realized.

Apologies if this has been posted elsewhere - my search did not turn up a relevant answer. I have an issues with JFreeChart annotations - I would like to draw one of several Shapes at a given size, say 10x10 pixels. However, the Annotation API appears to require data space coordinates. I am able to ...