Question mark inside a box in system text

Restore Standard Fonts only does its work to the two system font locations; the /System/Library/Fonts/ folder, and the root /Library/Fonts/ folder. Since the command did nothing to change the issue, then the most likely scenario left is that you have conflicting, or damaged fonts in your user account.

From the desktop (so Finder is the name of the foreground app next to the Apple log at the upper left), hold the Option key and choose Go > Library from the top menu bar. This will open the Library folder in your user account.

Open the Fonts folder you find there. Create a new folder on the desktop. Move, not copy, all fonts out of the Fonts folder into the new empty folder. Restart in Safe Mode and then restart normally.

Maybe the empty fonts folder has something to do with this.

If it's empty, it can't. The assumption (since the other two Fonts folder had been reset to OS X included fonts only with Restore Standard Fonts) was that the problem was most likely to be conflicting fonts in your account.

The Terminal command removes all font cache files from the system. Both for the system, and those for the user account you're in at the time. So that's not it. Or at least, not something that simple.

You're kind of down to two things:

1) Create a new user account and login to it. If the issue is cleared up there, then the problem is somewhere in your normal user account. If it's the same, it's a system wide issue.

2) If it is system wide, then I would suggest reinstalling the OS. That will replace all fonts and all system files with fresh copies. Make sure to do a backup before proceeding. A way back to at least where you were is very important if the reinstall somehow goes badly.

Please read this whole message before doing anything.

This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.

The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.

Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards, if applicable. Start up in safe mode and log in to the account with the problem.

Note: If FileVault is enabled in OS X 10.9 or earlier, or if a firmware password is set, or if the startup volume is a software RAID, you can’t do this. Ask for further instructions.

Safe mode is much slower to start up and run than normal, with limited graphics performance, and some things won’t work at all, including sound output and Wi-Fi on certain models. The next normal startup may also be somewhat slow.

The login screen appears even if you usually login automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.

Test while in safe mode. Same problem?

After testing, restart as usual (not in safe mode) and verify that you still have the problem. Post the results of the test.