Hello David, indeed, multiline variables do not work with Automake. In a future release, the substituted multiline value should be escaped by default, so that the resulting makefile works correctly.
In the meantime, there is a workaround available: use the undocumented macro _AM_SUBST_NOTMAKE([FOO]) to instruct automake that this variable is to be omitted from the generated Makefile.in. Sorry for the inconvenience, Stepan Kasal