My guess is that the solution, at least until libtool is improved to not
explicitly mark libltdl symbols for export when compiling libltdl as a
convenience library, is to either also mark all your symbols for export, or to
add this to your Makefile.am (which is what I did for M4):
# The -export-symbols-regex ".*" is a hack to work around the
# fact that on cygwin, the convenience library libltdl exports symbols,
# which effectively disables the auto-exporting of all other symbols.
# Revisit this if libtool on cygwin improves.
# See http://lists.gnu.org/archive/html/libtool-patches/2007-02/msg00062.html
AM_LDFLAGS += -export-symbols-regex ".*"