rectification problems

We are having problems rectifying rasterized contour maps.
The raster maps consist of one-pixel-wide contour lines, and
we are rectifying them into a UTM coordinate system; we
then want to run r.surf.contour on the rectified map. We
have found, however, that when we rectify, the contour lines
become discontinuous -- occasionally pixels drop out,
leading to problems with r.surf.contour. Does anyone know
a way either to ensure that pixels do not drop out in
rectification, or to fix slightly discontinuous lines in a
contour map without editing them by hand (the maps are
large, > 5k x 5k). Unfortunately it is probably impossible to
import them as vectors and then rasterize them in GRASS;
we would much rather import the large raster files. Any help
would be greatly appreciated. Thanks --

Nick Cahill
Perseus Project
nick@ikaros.harvard.edu