I added the following lines to BBBToolchain.cmake for pkg-config to work properly:
# adjust pkg-config
set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}\;${CMAKE_SYSROOT}/usr/lib/pkgconfig\;${CMAKE_SYSROOT}/usr/lib/arm-linux-gnueabihf/pkgconfig\;${CMAKE_SYSROOT}/usr/share/pkgconfig")
set(ENV{PKG_CONFIG_LIBDIR} "${CMAKE_SYSROOT}/usr/lib/arm-linux-gnueabihf/pkgconfig\;${CMAKE_SYSROOT}/usr/share/pkgconfig")
set(ENV{PKG_CONFIG_SYSROOT_DIR} ${CMAKE_SYSROOT})
# required on Windows - extra flag to pkg-config
if(WIN32)
set(PKG_CONFIG_ARGN "--dont-define-prefix")
endif(WIN32)