This is actually a bug (different variable names in FindFLAC.cmake and CMakeLists.txt) that was fixed implicitly upstream with http://repo.or.cz/alure.git/commit/6934c17f9ace7fc19ea94623dab0a4b37d11a879
I added a patch for v1.2 and also included support for fluidsynth. Now all dependencies that are available in the Cygwin repos are built.
