I can confirm this behavior, on both Inkscape 0.91 and 0.92.
This behavior it is known to the Inkscape team, but I don’t know if this is regarded as a “bug” or not– it may be considered a predictable artifact of the rendering method that is used. See here, for example: http://tavmjong.free.fr/blog/?p=1257
If you’d like to ask the Inkscape team about this, I’d suggest starting with a question at https://answers.launchpad.net/inkscape , rather than filing a bug report. (Of course, filing a bug report wouldn’t be out of the question– this is “unexpected” behavior.)
However, none of that really answers your fundamental issue here. The “right” solution is neither to worry about the rendering, nor to fill circles slowly, but to draw fast, filled circles within StippleGen. My solution to this is to replace each hollow circle with a single spiral, which can be plotted quite quickly.