diff --git a/src/application.coffee b/src/application.coffee
index 95306d67..2af00807 100644
--- a/src/application.coffee
+++ b/src/application.coffee
@@ -291,16 +291,17 @@ specialActionEnvVars =
 executedSpecialActionEnvVars = {}
 
 executeSpecialActionsAndBootConfig = (env) ->
-	_.map specialActionEnvVars, (specialActionCallback, key) ->
-		if env[key]? && specialActionCallback?
-			# This makes the Special Action Envs only trigger their functions once.
-			if !_.has(executedSpecialActionEnvVars, key) or executedSpecialActionEnvVars[key] != env[key]
-				specialActionCallback(env[key])
-				executedSpecialActionEnvVars[key] = env[key]
-	bootConfigVars = _.pick env, (val, key) ->
-		return _.startsWith(key, device.bootConfigEnvVarPrefix)
-	if !_.isEmpty(bootConfigVars)
-		device.setBootConfig(bootConfigVars)
+	Promise.try ->
+		_.map specialActionEnvVars, (specialActionCallback, key) ->
+			if env[key]? && specialActionCallback?
+				# This makes the Special Action Envs only trigger their functions once.
+				if !_.has(executedSpecialActionEnvVars, key) or executedSpecialActionEnvVars[key] != env[key]
+					specialActionCallback(env[key])
+					executedSpecialActionEnvVars[key] = env[key]
+		bootConfigVars = _.pick env, (val, key) ->
+			return _.startsWith(key, device.bootConfigEnvVarPrefix)
+		if !_.isEmpty(bootConfigVars)
+			device.setBootConfig(bootConfigVars)
 
 UPDATE_IDLE = 0
 UPDATE_UPDATING = 1
@@ -372,10 +373,6 @@ application.update = update = (force) ->
 				remoteApps = _.indexBy(remoteApps, 'appId')
 				remoteAppIds = _.keys(remoteApps)
 
-				# Run special functions against variables if remoteAppEnvs has the corresponding variable function mapping.
-				_.map remoteAppIds, (appId) ->
-					executeSpecialActionsAndBootConfig(remoteAppEnvs[appId])
-
 				apps = _.indexBy(apps, 'appId')
 				localApps = _.mapValues apps, (app) ->
 					app.env = JSON.stringify(_.omit(JSON.parse(app.env), _.keys(specialActionEnvVars)))
@@ -395,7 +392,11 @@ application.update = update = (force) ->
 
 				allAppIds = _.union(localAppIds, remoteAppIds)
 
-				Promise.map allAppIds, (appId) ->
+				# Run special functions against variables if remoteAppEnvs has the corresponding variable function mapping.
+				Promise.map remoteAppIds, (appId) ->
+					executeSpecialActionsAndBootConfig(remoteAppEnvs[appId])
+				.return(allAppIds)
+				.map (appId) ->
 					Promise.try ->
 						fetch(remoteApps[appId]) if _.includes(toBeDownloaded, appId)
 					.then ->
@@ -468,7 +469,8 @@ application.initialize = ->
 	.then (apps) ->
 		Promise.map apps, (app) ->
 			executeSpecialActionsAndBootConfig(JSON.parse(app.env))
-			unlockAndStart(app)
+			.then ->
+				unlockAndStart(app)
 	.catch (error) ->
 		console.error('Error starting apps:', error)
 	.then ->
diff --git a/src/device.coffee b/src/device.coffee
index e07f9f26..d68cf951 100644
--- a/src/device.coffee
+++ b/src/device.coffee
@@ -8,7 +8,7 @@ config = require './config'
 configPath = '/boot/config.json'
 request = Promise.promisifyAll(require('request'))
 execAsync = Promise.promisify(require('child_process').exec)
-
+fs = Promise.promisifyAll(require('fs'))
 exports.getID = do ->
 	deviceIdPromise = null
 	return ->
@@ -39,7 +39,9 @@ rebootDevice = ->
 	request.postAsync(config.gosuperAddress + '/v1/reboot')
 
 exports.bootConfigEnvVarPrefix = bootConfigEnvVarPrefix = 'RESIN_HOST_CONFIG_'
-bootConfigPath = '/mnt/root/boot/config.txt'
+bootBlockDevice = '/dev/mmcblk0p1'
+bootMountPoint = '/mnt/root/boot'
+bootConfigPath = bootMountPoint + '/config.txt'
 configRegex = new RegExp('(' + _.escapeRegExp(bootConfigEnvVarPrefix) + ')(.+)')
 forbiddenConfigKeys = [
 	'disable_commandline_tags'
@@ -61,7 +63,7 @@ forbiddenConfigKeys = [
 parseBootConfigFromEnv = (env) ->
 	# We ensure env doesn't have garbage
 	parsedEnv = _.pick env, (val, key) ->
-		return _.startsWith(bootConfigEnvVarPrefix)
+		return _.startsWith(key, bootConfigEnvVarPrefix)
 	parsedEnv = _.mapKeys parsedEnv, (val, key) ->
 		key.replace(configRegex, '$2')
 	parsedEnv = _.omit(parsedEnv, forbiddenConfigKeys)
@@ -102,7 +104,9 @@ exports.setBootConfig = (env) ->
 					configStatement = configStatements[index]
 				return configStatement
 			# Here's the dangerous part:
-			fs.writeFileAsync(bootConfigPath + '.new', outputConfig.join('\n'))
+			execAsync("mount -t vfat -o remount,rw #{bootBlockDevice} #{bootMountPoint}")
+			.then ->
+				fs.writeFileAsync(bootConfigPath + '.new', outputConfig.join('\n'))
 			.then ->
 				fs.renameAsync(bootConfigPath + '.new', bootConfigPath)
 			.then ->