I looked at the SVG, and it seems you are making the zones in the wrong way. Only in Illustrator does a group layer called win-zones/death-zones/fortress-zones filled with circles work. Inkscape outputs circle elements as a Path element using a path command we don't support yet. See
this post on how to make zones properly in Inkscape.
So, besides that, your map is being outputted correctly – the “zones” as you have them now are being interpreted as walls.
Edit: Oh, and you have duplicated “zones” on the upper part of the SVG.