Seems that the only other option with Inkscape itself (saving as 'Plain SVG', converting the plain SVG to PDF) fails because somehow the fix for bug #500440 got lost with 0.48.2 and later versions.
You could try running scour [1] as standalone python script to convert the SVG files to 'Optimized SVG' (can't be scripted via cli), and then convert that optimized SVG to PDF (via inkscape cli).
[1] Scour.py is used by Inkscape as output extension for 'Optimized SVG' and has lots of options to clean SVG files.
<http://codedread.com/scour/>
Seems that the only other option with Inkscape itself (saving as 'Plain SVG', converting the plain SVG to PDF) fails because somehow the fix for bug #500440 got lost with 0.48.2 and later versions.
You could try running scour [1] as standalone python script to convert the SVG files to 'Optimized SVG' (can't be scripted via cli), and then convert that optimized SVG to PDF (via inkscape cli).
[1] Scour.py is used by Inkscape as output extension for 'Optimized SVG' and has lots of options to clean SVG files. codedread. com/scour/>
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