Now that I got everything sorted out (thanks to all who replied!), I figure I might as well post to the list how I automated Inkscape SVG exporting under Windows+cygwin, perhaps it will save someone else some time in the future. I use GNU "make" to build my documents, and here are the relevant bits of the Makefile:
------ INKSCAPE=d:/portable_apps/inkscape/inkscape.exe SRCDIR=$(shell cygpath -d -m `pwd`)
%.pdf: %.svg $(INKSCAPE) -f $(SRCDIR)/$< -A $(SRCDIR)/$@
# list of PDFs to build from SVGs: all: foo.pdf bar.pdf baz.pdf ------
The first stumbling block was that inkscape requires full paths to the original file and the destination file. The second stumbling block was how to translate them for inkscape, which does not like cygwin's /cygdrive/c/... notation.
The above is not optimal, so if anybody spots better ways to go about things, let me know. I just have to figure out how to avoid hardcoding the path to inkscape, which is in different directories on my various machines...