I've noticed this problem also, and instead of using some code in my application to correct the positioning i've found out that the following works for me:
- Open up the xml editor (ctrl+shift+x)
- Repeat the following step for each of the lines that contain a <svg:g> tag
- Press ctrl+shift+g to ungroup the grouped objects, this will cause inkscape to apply the transformation directly to the coordinates
- After you've ungrouped all the groups you can start grouping again, the transforms won't be applied a second time
I've noticed this problem also, and instead of using some code in my application to correct the positioning i've found out that the following works for me:
- Open up the xml editor (ctrl+shift+x)
- Repeat the following step for each of the lines that contain a <svg:g> tag
- Press ctrl+shift+g to ungroup the grouped objects, this will cause inkscape to apply the transformation directly to the coordinates
- After you've ungrouped all the groups you can start grouping again, the transforms won't be applied a second time