I'm not sure off-hand, and for some reason your attached image hasn't come through. Could you attach the EPS file, or perhaps better, the .SVG file after you've scaled (but before you've used PixelSnap)?
Also, for your info: I'm not really maintaining PixelSnap these days. It was a great idea, but the fact that Inkscape's Python extensions are non-interactive, and fairly slow (due to having to re-process the whole SVG file and feed the entire output back into inkscape) has put me off somewhat. One day, I'll get around to making some integrated inkscape code for it.
But I'll do what I can find time for to investigate your issue.