diff --git a/initrd/bin/config-gui.sh b/initrd/bin/config-gui.sh
index 67c5fbfa..55b3831c 100755
--- a/initrd/bin/config-gui.sh
+++ b/initrd/bin/config-gui.sh
@@ -2,7 +2,7 @@
 #
 set -e -o pipefail
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 file_selector() {
   FILE=""
@@ -49,15 +49,6 @@ file_selector() {
     exit 1
   fi
 }
-replace_config() {
-  CONFIG_OPTION=$1
-  NEW_SETTING=$2
-
-  awk "gsub(\"^export ${CONFIG_OPTION}=.*\",\"export ${CONFIG_OPTION}=\\\"${NEW_SETTING}\\\"\")" /etc/config > /tmp/config
-  awk "gsub(\"^${CONFIG_OPTION}=.*\",\"${CONFIG_OPTION}=\\\"${NEW_SETTING}\\\"\")" /etc/config >> /tmp/config
-  grep -v "^export ${CONFIG_OPTION}=" /etc/config | grep -v "^${CONFIG_OPTION}=" >> /tmp/config
-  mv /tmp/config /etc/config
-}
 
 while true; do
   unset menu_choice
@@ -76,7 +67,7 @@ while true; do
       exit 0
     ;;
     "b" )
-      CURRENT_OPTION=`grep 'CONFIG_BOOT_DEV=' /etc/config | cut -f2 -d '=' | tr -d '"'`
+      CURRENT_OPTION=`grep 'CONFIG_BOOT_DEV=' /tmp/config | cut -f2 -d '=' | tr -d '"'`
       find /dev -name 'sd*' -o -name 'nvme*' > /tmp/filelist.txt
       file_selector "/tmp/filelist.txt" "Choose the default /boot device.\n\nCurrently set to $CURRENT_OPTION."
       if [ "$FILE" == "" ]; then
@@ -85,7 +76,8 @@ while true; do
         SELECTED_FILE=$FILE
       fi
 
-      replace_config "CONFIG_BOOT_DEV" "$SELECTED_FILE"
+      replace_config /etc/config.user "CONFIG_BOOT_DEV" "$SELECTED_FILE"
+      combine_configs
 
       whiptail --title 'Config change successful' \
         --msgbox "The /boot device was successfully changed to $SELECTED_FILE" 16 60
@@ -94,7 +86,7 @@ while true; do
       whiptail --title 'Insert a USB thumb drive' \
         --msgbox "Insert a USB thumb drive so we can detect the device" 16 60
       mount-usb
-      CURRENT_OPTION=`grep 'CONFIG_USB_BOOT_DEV=' /etc/config | cut -f2 -d '=' | tr -d '"'`
+      CURRENT_OPTION=`grep 'CONFIG_USB_BOOT_DEV=' /tmp/config | cut -f2 -d '=' | tr -d '"'`
       find /dev -name 'sd*' -o -name 'nvme*' > /tmp/filelist.txt
       file_selector "/tmp/filelist.txt" "Choose the default USB boot device.\n\nCurrently set to $CURRENT_OPTION."
       if [ "$FILE" == "" ]; then
@@ -103,7 +95,8 @@ while true; do
         SELECTED_FILE=$FILE
       fi
 
-      replace_config "CONFIG_USB_BOOT_DEV" "$SELECTED_FILE"
+      replace_config /etc/config.user "CONFIG_USB_BOOT_DEV" "$SELECTED_FILE"
+      combine_configs
 
       whiptail --title 'Config change successful' \
         --msgbox "The USB boot device was successfully changed to $SELECTED_FILE" 16 60
@@ -116,10 +109,10 @@ while true; do
         exit 1
       fi
 
-      if (cbfs -o /tmp/config-gui.rom -l | grep -q "heads/initrd/etc/config") then
-        cbfs -o /tmp/config-gui.rom -d "heads/initrd/etc/config"
+      if (cbfs -o /tmp/config-gui.rom -l | grep -q "heads/initrd/etc/config.user") then
+        cbfs -o /tmp/config-gui.rom -d "heads/initrd/etc/config.user"
       fi
-      cbfs -o /tmp/config-gui.rom -a "heads/initrd/etc/config" -f /etc/config
+      cbfs -o /tmp/config-gui.rom -a "heads/initrd/etc/config.user" -f /etc/config.user
 
       if (whiptail --title 'Update ROM?' \
           --yesno "This will reflash your BIOS with the updated version\n\nDo you want to proceed?" 16 90) then
diff --git a/initrd/bin/flash-gui.sh b/initrd/bin/flash-gui.sh
index 191d977b..277a4fae 100755
--- a/initrd/bin/flash-gui.sh
+++ b/initrd/bin/flash-gui.sh
@@ -2,7 +2,7 @@
 #
 set -e -o pipefail
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 mount_usb(){
 # Mount the USB boot device
diff --git a/initrd/bin/flash.sh b/initrd/bin/flash.sh
index 4b70ac8a..e89c9a98 100755
--- a/initrd/bin/flash.sh
+++ b/initrd/bin/flash.sh
@@ -4,7 +4,7 @@
 #
 set -e -o pipefail
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 case "$CONFIG_BOARD" in
   librem* )
diff --git a/initrd/bin/generic-init b/initrd/bin/generic-init
index c0808e48..b63b0a05 100755
--- a/initrd/bin/generic-init
+++ b/initrd/bin/generic-init
@@ -2,7 +2,7 @@
 # Boot from a local disk installation
 
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 mount_boot()
 {
diff --git a/initrd/bin/gui-init b/initrd/bin/gui-init
index 20f12280..32dfc920 100755
--- a/initrd/bin/gui-init
+++ b/initrd/bin/gui-init
@@ -4,7 +4,7 @@
 CONFIG_BOOT_GUI_MENU_NAME='Heads Boot Menu'
 
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 mount_boot()
 {
diff --git a/initrd/bin/kexec-boot b/initrd/bin/kexec-boot
index 7d7d8367..49e48aee 100755
--- a/initrd/bin/kexec-boot
+++ b/initrd/bin/kexec-boot
@@ -1,7 +1,7 @@
 #!/bin/sh
 # Launches kexec from saved configuration entries
 set -e -o pipefail
-. /etc/config
+. /tmp/config
 . /etc/functions
 
 dryrun="n"
diff --git a/initrd/bin/kexec-iso-init b/initrd/bin/kexec-iso-init
index 755ebba6..ebe48fe0 100755
--- a/initrd/bin/kexec-iso-init
+++ b/initrd/bin/kexec-iso-init
@@ -2,7 +2,7 @@
 # Boot from signed ISO
 set -e -o pipefail
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 MOUNTED_ISO_PATH="$1"
 ISO_PATH="$2"
diff --git a/initrd/bin/kexec-save-default b/initrd/bin/kexec-save-default
index 0bbaa100..85ac3f27 100755
--- a/initrd/bin/kexec-save-default
+++ b/initrd/bin/kexec-save-default
@@ -1,7 +1,7 @@
 #!/bin/sh
 # Save these options to be the persistent default
 set -e -o pipefail
-. /etc/config
+. /tmp/config
 . /etc/functions
 
 while getopts "b:d:p:i:" arg; do
diff --git a/initrd/bin/kexec-seal-key b/initrd/bin/kexec-seal-key
index da5a187e..f574b558 100755
--- a/initrd/bin/kexec-seal-key
+++ b/initrd/bin/kexec-seal-key
@@ -11,7 +11,7 @@ TPM_SEALED="/tmp/secret/secret.sealed"
 RECOVERY_KEY="/tmp/secret/recovery.key"
 
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 paramsdir=$1
 if [ -z "$paramsdir" ]; then
diff --git a/initrd/bin/kexec-select-boot b/initrd/bin/kexec-select-boot
index 4a1f2a73..ab8002fe 100755
--- a/initrd/bin/kexec-select-boot
+++ b/initrd/bin/kexec-select-boot
@@ -1,7 +1,7 @@
 #!/bin/sh
 # Generic configurable boot script via kexec
 set -e -o pipefail
-. /etc/config
+. /tmp/config
 . /etc/functions
 
 add=""
diff --git a/initrd/bin/kexec-sign-config b/initrd/bin/kexec-sign-config
index 1ff9f46c..23cdf28d 100755
--- a/initrd/bin/kexec-sign-config
+++ b/initrd/bin/kexec-sign-config
@@ -1,7 +1,7 @@
 #!/bin/sh
 # Sign a valid directory of kexec params
 set -e -o pipefail
-. /etc/config
+. /tmp/config
 . /etc/functions
 
 rollback="n"
diff --git a/initrd/bin/usb-init b/initrd/bin/usb-init
index 5ddfdff1..4a52b262 100755
--- a/initrd/bin/usb-init
+++ b/initrd/bin/usb-init
@@ -2,7 +2,7 @@
 # Boot a USB installation
 
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 if [ "$CONFIG_TPM" = "y" ]; then
 	# Extend PCR4 as soon as possible
diff --git a/initrd/bin/usb-scan b/initrd/bin/usb-scan
index 57f6879b..6d3eda27 100755
--- a/initrd/bin/usb-scan
+++ b/initrd/bin/usb-scan
@@ -2,7 +2,7 @@
 # Scan for USB installation options
 set -e -o pipefail
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 # Unmount any previous boot device
 if grep -q /boot /proc/mounts ; then
diff --git a/initrd/bin/x230-flash.init b/initrd/bin/x230-flash.init
index a4d22c0f..e02dcf5d 100755
--- a/initrd/bin/x230-flash.init
+++ b/initrd/bin/x230-flash.init
@@ -3,7 +3,7 @@
 # invoke a recovery shell and prompt the user for how to proceed
 
 . /etc/functions
-. /etc/config
+. /tmp/config
 
 insmod /lib/modules/ehci-hcd.ko
 insmod /lib/modules/ehci-pci.ko
diff --git a/initrd/etc/functions b/initrd/etc/functions
index 4488476a..e556c960 100755
--- a/initrd/etc/functions
+++ b/initrd/etc/functions
@@ -217,3 +217,20 @@ preserve_rom() {
 		fi
 	done
 }
+replace_config() {
+  CONFIG_FILE=$1
+  CONFIG_OPTION=$2
+  NEW_SETTING=$3
+
+# first pull out the existing option from the global config and place in a tmp file
+  awk "gsub(\"^export ${CONFIG_OPTION}=.*\",\"export ${CONFIG_OPTION}=\\\"${NEW_SETTING}\\\"\")" /tmp/config > ${CONFIG_FILE}.tmp
+  awk "gsub(\"^${CONFIG_OPTION}=.*\",\"${CONFIG_OPTION}=\\\"${NEW_SETTING}\\\"\")" /tmp/config >> ${CONFIG_FILE}.tmp
+
+# then copy any remaining settings from the existing config file, minus the option you changed
+  grep -v "^export ${CONFIG_OPTION}=" ${CONFIG_FILE} | grep -v "^${CONFIG_OPTION}=" >> ${CONFIG_FILE}.tmp
+
+  mv ${CONFIG_FILE}.tmp ${CONFIG_FILE}
+}
+combine_configs() {
+	sort /etc/config* | uniq > /tmp/config
+}
diff --git a/initrd/init b/initrd/init
index d489f6ae..4410c6fb 100755
--- a/initrd/init
+++ b/initrd/init
@@ -40,7 +40,8 @@ hwclock -l -s
 
 # Read the system configuration parameters
 . /etc/functions
-. /etc/config
+combine_configs
+. /tmp/config
 
 # Add our boot devices into the /etc/fstab, if they are defined
 # in the configuration file.