Some recent Windows 8.1 updates (particularly KB2993651) has been seen to break modifier key functionality in an Allegro 4 application I develop. There's also a third party application with some discussion about it here:
http://synergy-project.org/spit/issues/details/4125/
It's not necessarily something the Allegro developers can do anything about, but they should still be aware of it. I don't know if Allegro 5 is affected by this problem.
Just to follow up, the key[] array does still detect modifier key presses correctly, and I changed the A4 application to use it instead of key_shifts to check for CTRL, ALT and SHIFT and the problem is bypassed entirely. This means Allegro can still detect those keypresses and key_shifts may be able to be handled differently to defeat the Windows update-induced bug.