diff --git a/src/etc/inc/system.inc b/src/etc/inc/system.inc
index 63720fe47..193bd5c93 100644
--- a/src/etc/inc/system.inc
+++ b/src/etc/inc/system.inc
@@ -888,6 +888,9 @@ function system_webgui_start()
 
 	@unlink("{$g['varrun_path']}/lighty-webConfigurator.pid");
 
+	/* regenerate the php.ini files in case the setup has changed */
+	mwexec('/usr/local/etc/rc.php_ini_setup');
+
 	/* attempt to start lighthttpd */
 	$res = mwexec("/usr/local/sbin/lighttpd -f {$g['varetc_path']}/lighty-webConfigurator.conf");
 
diff --git a/src/etc/rc b/src/etc/rc
index b3a8a10af..19747e348 100755
--- a/src/etc/rc
+++ b/src/etc/rc
@@ -307,7 +307,7 @@ echo "done."
 # Recreate capabilities DB
 /usr/bin/cap_mkdb /etc/login.conf
 
-# Run the php.ini setup file
+# Set up the correct php.ini content
 /usr/local/etc/rc.php_ini_setup
 
 chmod u+rx  /usr/local/opnsense/service/configd.py
diff --git a/src/etc/rc.initial.firmware b/src/etc/rc.initial.firmware
index 09a132a14..fb06a4e46 100755
--- a/src/etc/rc.initial.firmware
+++ b/src/etc/rc.initial.firmware
@@ -47,7 +47,6 @@ pkg upgrade -y
 echo
 
 # restart the GUI after PHP changes have been applied
-/usr/local/etc/rc.php_ini_setup
 /usr/local/etc/rc.restart_webgui
 
 echo
diff --git a/src/opnsense/scripts/pkg_upgrade.sh b/src/opnsense/scripts/pkg_upgrade.sh
index c1aa51ae6..5214fa56d 100755
--- a/src/opnsense/scripts/pkg_upgrade.sh
+++ b/src/opnsense/scripts/pkg_upgrade.sh
@@ -36,25 +36,20 @@ PKG_PROGRESS_FILE=/tmp/pkg_upgrade.progress
 if [ -z "$pkg_running" ]; then
 	echo "***GOT REQUEST TO UPGRADE: $package***" >> ${PKG_PROGRESS_FILE}
 	if [ "$package" == "all" ]; then
-	    # start pkg upgrade
-	    echo '***STARTING UPGRADE***' >> ${PKG_PROGRESS_FILE}
+		echo '***STARTING UPGRADE***' >> ${PKG_PROGRESS_FILE}
 		pkg upgrade -y >> ${PKG_PROGRESS_FILE}
-		echo '***CHECKING FOR MORE UPGRADES, CAN TAKE 30 SECONDS***' >> ${PKG_PROGRESS_FILE}
-		/usr/local/opnsense/scripts/pkg_updatecheck.sh
-		echo '***DONE***' >> ${PKG_PROGRESS_FILE}
 	else
-		# start pkg upgrade
-	    echo '***STARTING UPGRADE - ONE PACKAGE***' >> ${PKG_PROGRESS_FILE}
+		# XXX this is dangerous and not recommended by pkgng devs
+		echo '***STARTING UPGRADE - ONE PACKAGE***' >> ${PKG_PROGRESS_FILE}
 		pkg upgrade -y $package >> ${PKG_PROGRESS_FILE}
-		echo '***CHECKING FOR MORE UPGRADES, CAN TAKE 30 SECONDS***' >> ${PKG_PROGRESS_FILE}
-		/usr/local/opnsense/scripts/pkg_updatecheck.sh
-		echo '***DONE***' >> ${PKG_PROGRESS_FILE}
 	fi
+	echo '***CHECKING FOR MORE UPGRADES, CAN TAKE 30 SECONDS***' >> ${PKG_PROGRESS_FILE}
+	/usr/local/opnsense/scripts/pkg_updatecheck.sh
 	# remove no longer referenced packages
 	pkg autoremove -y >> ${PKG_PROGRESS_FILE}
-	# regenerate php.ini and restart the web server
-	/usr/local/etc/rc.php_ini_setup >> ${PKG_PROGRESS_FILE}
+	# restart the web server
 	/usr/local/opnsense/service/configd_ctl.py 'service restart webgui' >> ${PKG_PROGRESS_FILE}
+	echo '***DONE***' >> ${PKG_PROGRESS_FILE}
 else
 	echo 'Upgrade already in progress' >> ${PKG_PROGRESS_FILE}
 	echo '***DONE***' >> ${PKG_PROGRESS_FILE}