It is one of FZ's idiosyncrasies... FZ doesn't like transformed circles... Your circles need to have "0" orientation. If you rotate your circles or do anything that will cause them to have the transformed parameters in the .svg, your circle will have the single red center. wired... 
If you take a part in your pcb, i.e. that has 8 connectors (circles), and rotate it 90 deg., then all 8 circles will be transformed (rotated). "FZ treats transformed circles differently than non-transformed circles"
To solve the problem; you either need to un-transform (correct the circles back to their original form/orientation. or draw a new circle and replace it. 