diff --git a/bootstrap b/bootstrap
index d0ee9fa39c..6a5ea7e069 100755
--- a/bootstrap
+++ b/bootstrap
@@ -649,12 +649,17 @@ for a in ${KWSYS_CXX_SOURCES}; do
   echo "	${cmake_cxx_compiler} ${cmake_cxx_flags} -DKWSYS_NAMESPACE=cmsys -c ${src} -o ${a}.o" >> "${cmake_bootstrap_dir}/Makefile"
 done
 
-# Write prefix to Bootstrap.cmk/InitialCacheFlags.cmake
+# Write our default settings to Bootstrap.cmk/InitialCacheFlags.cmake.
 cat > "${cmake_bootstrap_dir}/InitialCacheFlags.cmake" <<EOF
 # Generated by ${cmake_source_dir}/bootstrap
+# Default cmake settings.  These may be overridden any settings below.
+SET (CMAKE_INSTALL_PREFIX "${cmake_prefix_dir}" CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
+SET (CMAKE_DOC_DIR "${cmake_doc_dir}" CACHE PATH "Install location for documentation (relative to prefix)." FORCE)
+SET (CMAKE_MAN_DIR "${cmake_man_dir}" CACHE PATH "Install location for man pages (relative to prefix)." FORCE)
+SET (CMAKE_DATA_DIR "${cmake_data_dir}" CACHE PATH "Install location for data (relative to prefix)." FORCE)
 EOF
 
-# Start with user-specified settings.  Handle relative-path case for
+# Add user-specified settings.  Handle relative-path case for
 # specification of cmake_init_file.
 (
 cd "${cmake_binary_dir}"
@@ -663,16 +668,6 @@ if [ -f "${cmake_init_file}" ]; then
 fi
 )
 
-# Add our default settings.
-cat >> "${cmake_bootstrap_dir}/InitialCacheFlags.cmake" <<EOF
-
-# Default cmake settings.  These will not override any settings above.
-SET (CMAKE_INSTALL_PREFIX "${cmake_prefix_dir}" CACHE PATH "Install path prefix, prepended onto install directories.")
-SET (CMAKE_DOC_DIR "${cmake_doc_dir}" CACHE PATH "Install location for documentation (relative to prefix).")
-SET (CMAKE_MAN_DIR "${cmake_man_dir}" CACHE PATH "Install location for man pages (relative to prefix).")
-SET (CMAKE_DATA_DIR "${cmake_data_dir}" CACHE PATH "Install location for data (relative to prefix).")
-EOF
-
 echo "---------------------------------------------"
 
 # Run make to build bootstrap cmake
@@ -702,4 +697,4 @@ export MAKE
 echo "---------------------------------------------"
 
 # And we are done. Now just run make
-echo "CMake is configured. Now just run ${cmake_make_processor}."
+echo "CMake has bootstrapped.  Now run ${cmake_make_processor}."