The file AvogadroConfig.cmake installed to the users system contains broken paths for Avogadro_BUILD_SETTINGS_FILE and Avogadro_USE_FILE (in my case e.g. /usr//AvogadroUse.cmake). I guess this is because of
@CMAKE_INSTALL_PREFIX@/@PLUGIN_INSTALL_DIR@
which should probably be
@CMAKE_INSTALL_PREFIX@/@Avogadro_PLUGIN_INSTALL_DIR@
I will fix that now. Had to change the name of that variable and forgot to change it here too. Thanks for pointing this out.