Alas, inkscape (and probably other programs) breaks things in much the same ways. It ignores its initial working directory, and instead maintains two distinct "working directories" for saving and opening, which are preserved across instances of inkscape and unaffected by the location of the file currently being edited.
Having recently used inkscape a bit, this was *very* frustrating. It'd be lovely if our GUI programs could use the "folder" approach nicely...