Thank you for such a prompt reply. I have just upgraded my Inkscape to 0.48.5 and this alone seems to have solved the problem. I will, however, set the transformation to optimised as you recommended. Thank you.
All the best!

I'm putting together some figures for my thesis and keep encountering the same problem. I process SVG images exported from various analysis software. The processing usually involves annotation and resizing that doesn't preserve the original aspect ratio. The final figures look fine in Inkscape, but ...