As a consequence of this bug report
http://lists.gnu.org/archive/html/bug-gnu-chess/2009-08/msg00000.html
I started working on the GnuChess source to
(1) fix bugs like the ones above;
(2) make gnuchess compliant with the modern
Chess Engine Communication Protocol as described here
http://home.hccnet.nl/h.g.muller/engine-intf.html
(3) make the GnuChess source more object oriented;
(4) implement modern search ideas (like Late Move Reductions).
My latest version can be found here
http://alpha.uhasselt.be/Research/Algebra/Toga/gnuchess-release/
See also this post on the Winboard Forum
http://www.open-aurec.com/wbforum/viewtopic.php?f=2&t=50422&start=80
which contains further details and some data on strength improvement.
Give it a try!