I have this bug with inkscape 0.48.3.1-1.1 and libgnomevfs2-0 1:2.24.4-1. The suggested fix, uncommenting the line "file: file" in /etc/gnome-vfs-2.0/modules/default-modules.conf, has resolved the issue. The SVG file I was originally trying to open was created with inkscape 0.45.1: /usr/share/kde4/apps/kgoldrunner/themes/default/set.svg from kgoldrunner 4:4.8.4-1. I suspect the issue would happen with any SVG file, but I cannot go back to the old behaviour now by re-commenting-out the "file: file" line, so I do not know for sure.
Here is the error message reproduced for completeness: $ inkscape default/set.svg (inkscape:21058): libgnomevfs-CRITICAL **: gnome_vfs_uri_is_local: assertion `uri != NULL' failed ** (inkscape:21058): WARNING **: Invalid URI ** (inkscape:21058): WARNING **: Error: Could not open file 'default/set.svg' with VFS
