Believe it or not, there are pens out there other than the Sharpie brand. I haven't used a Sharpie before to put a black gasket around N-scale windows, but I have used "art" pens and calligraphy pens, which use permanent, non-fading India Ink in them. No purpleness at all using these pens, and the ink does not run under Dullcote.
Buy 'em at Michael's or Hobby Lobby...or order from Dick Blick.
Try it, you'll like it....