Have you tried publishing to PDF and dropping the PDF into FontCreator?
If the circles are very small, there may not be enough nodes to create a near-perfect circle. The only solution to that is to increase the funits/em setting from 2048 to 4096 or 8192 for extremely finely detailed fonts. Very fine detail will not be seen at normal print sizes, only if enlarged to 72 point or beyond on posters.
For a nearly perfect circle, the best is what you get if you use the ellipse tool — a circle with four on-curve nodes and eight off-curve nodes. Eight points is not enough and sixteen is more than necessary.
