Okay, double check that you are configuring cmake appropriately, specifically setting the MAKE_INSTALL_PREFIX correctly.
mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/usr ../
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/indi_rpicam2x.xml CONFIGURATIONS Release DESTINATION ${INDI_DATA_DIR})
install( FILES ${CMAKE_CURRENT_BINARY_DIR}/indi_rpicam2x.xml DESTINATION ${INDI_DATA_DIR} )