We built Gtk# 2.12.3+ (from svn actually) using the gtk+ bundle in cygwin without issues. However you need to follow the wiki steps on Medsphere's site to make sure that cygwin is setup correctly. You actually want to build with gcc set to use the MinGW compiler, so as not to introduce a cygwin dependancy on the gtk-sharp glue libs.
There are some noticeable improvements in the updates. Jae
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