A few things could be the issue:

1.) Permissions Issue (this is a CONFIRMED bug in Windows 8/8.1 and later versions of 7). Change your UAC settings to as low as they go, mark yourself as the admin, and uncheck the read only box on the Program Files x86 folder. Reboot and try again. Make sure you don't have a firewall active on your computer or router. RUN AS THE ADMIN don't run it as a user. It will default you to user everytime (hence the issue). You can modify your read/write access in the security tab in the properties of the folder as well.

2.) Corrupted boot file/folder. You can find plenty of clean boot folders for ARR with a quick Google search. You will need read/write access to replace your corrupted boot files with the ones you downloaded (see 1).

3.) Registry/core/hardware issue. These are the ones that are difficult to fix. sfc /scannow and chkdisk may be your solution. If hardware, your HDD may be going bad and a new install will be required.

Make sure your firewall/antivirus is off or FFXIV is whitelisted as well.

When troubleshooting and modifying, do so only if you understand the risks as all of the steps above are a "do so at your own risk".