VPS（Ubuntu）からログアウトする（SSH接続を切る）と403エラーなどになる

環境
・さくらVPS
・Ubuntu 14.04.3 LTS
・Nginx 1.4.6
・Apache 2.4.7

Nginx でリバースプロキシを設定して、
Apache や Nodeアプリ を動かしている VPS がありました。
そちらを別の VPS に移行することになり、
その際に Ubuntu のバージョンも上げる事になったので、
いちから構築しなおしました。

とりあえず動くようになりましたが、
VPSからログアウトしてブラウザで確認すると
以下の様なエラーでてしましいます。

▼ Apacheで動いてるWebサーバーの場合

Forbidden
You don't have permission to access / on this server.
Apache/2.4.7 (Ubuntu) Server at xxxxx.xxxxx.xxx Port 80

▼ Nodeアプリの場合

Error: ENOENT: no such file or directory, open '/home/xxxxx/apps/filer/Manager.coffee'
  at Error (native)
  at Object.fs.openSync (fs.js:584:18)
  at Object.fs.readFileSync (fs.js:431:33)
  at Object.exports._compileFile (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:224:14)
  at getSourceMap (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:343:22)
  at getSourceMapping (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:351:19)
  at formatSourcePosition (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:303:16)
  at /home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:369:33
  at Function.Error.prepareStackTrace (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/coffee-script/lib/coffee-script/coffee-script.js:372:7)
  at next (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/node_modules/connect/lib/proto.js:150:16)
  at pass (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:107:24)
  at nextRoute (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:100:7)
  at callbacks (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:164:11)
  at callbacks (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:167:9)
  at param (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:135:11)
  at pass (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:142:5)
  at Router._dispatch (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:170:5)
  at Object.router (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/lib/router/index.js:33:10)
  at next (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/node_modules/connect/lib/proto.js:199:15)
  at next (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/node_modules/connect/lib/middleware/session.js:309:9)
  at /home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/express/node_modules/connect/lib/middleware/session.js:333:9
  at Command.callback (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/lib/connect-redis.js:91:9)
  at RedisClient.return_reply (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/node_modules/redis/index.js:664:25)
  at JavascriptReplyParser.reply_parser.send_reply (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/node_modules/redis/index.js:332:14)
  at JavascriptReplyParser.run (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/node_modules/redis/lib/parsers/javascript.js:132:18)
  at JavascriptReplyParser.execute (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/node_modules/redis/lib/parsers/javascript.js:107:10)
  at Socket.<anonymous> (/home/xxxxx/.nvm/versions/node/v5.5.0/lib/node_modules/connect-redis/node_modules/redis/index.js:131:27)
  at emitOne (events.js:90:13)
  at Socket.emit (events.js:182:7)
  at readableAddChunk (_stream_readable.js:147:16)
  at Socket.Readable.push (_stream_readable.js:111:10)
  at TCP.onread (net.js:523:20)

Nodeアプリのデーモン化は forever で対応しています。
（supervisor で対応したいのですが、上手く起動しなかったので）

再度VPSにログインすると正常に接続されるようになります。
なにか原因は考えられますでしょうか？