Figured it out - dumb mistake on my part mixed with completely useless error reporting about the problem in inkscape. I had tried to start it with
build\inkscape
and not
inkscape\inkscape
Of course it couldn't find anything in build\share and blew up. But since it was built with the default -mwindows switch the relevant error message never appeared in the console and only the mysterious VC++ message did. Found the issue after changing -mwindows to -mconsole in build.xml and rebuilding. With -mconsole there was an error message about a file with a build\share path not being found, and since there is no build\share, my error was revealed.
Sorry about the noise.
David Mathog mathog@...1176... Manager, Sequence Analysis Facility, Biology Division, Caltech