EPS does not support transparency, probably the cause of your troubles.
This will not fix your issue, but might be a workaround (perhaps preferred over psfrag):
Are you aware of the new EPS/PS/PDF+LaTeX save option? ftp://ftp.dante.de/tex-archive/info/svg-inkscape/InkscapePDFLaTeX.pdf
EPS does not support transparency, probably the cause of your troubles. dante.de/ tex-archive/ info/svg- inkscape/ InkscapePDFLaTe X.pdf
This will not fix your issue, but might be a workaround (perhaps preferred over psfrag):
Are you aware of the new EPS/PS/PDF+LaTeX save option?
ftp://ftp.