Cannot access /sdcard/ (internal storage)

After I got my phone restored from an nandroid backup, I found almost all apps cannot gain access to /sdcard/ (internal storage), including ES file manager, Z archiver and so on. When any of these apps access /sdcard/, or any other equivalent folders like /storage/emulated/0, /storage/emulated/legacy, /storage/sdcard0, they only shows a blank directory, and I cannot create any file or folder. When I try with the stock file manager (My files), it does show the files, but i cannot rename, edit, or create anything. Android File manager is able to copy most of my files out. But It stucks when I try to create a folder or send something. I tried to re-flash the same ROM again (which worked perfectly before), the issue remains. I have backed up important data from /sdcard/. In terminal emulator, cd sdcard, ls gives opendir failed: permission denied. Then I tried su, ls shows the correct directory. How should I fix it? Extra: I found a new folder called knox-emulated in /storage which is not there before. External SD card (/storage/extSdCard) works fine. Device Information: Samsung Galaxy Note 3, Android 4.4.2 Rooted, with a custom ROM modified based on the Stock ROM. Custom recovery installed.