This problem occured randomly but quite often and always happen after alt-tabbing.

After alt-tabbing when I get back to FFXIV windows, the program won't accept any keyboard input and clicks.

But if you hover your pointer above an icon, it will still react (showing icon name) but clicks and keypress are totally ignored and this only happen in FFXIV, if you alt tab back to Windows, mouse and keyboard work normally.

I found similiar problem in FFXIV 1.0 forum:
I can't find any solution to fix this issue, the only way to fix this is using task manager and kill the program which is annoying if you are doing something in game.

My system :
Intel Core i5-4460
MSI H97-Gaming 3
Geforce GTX 760
8 GB RAM
Windows 8.1
Playing in Windowed Fullscreen mode