I've been encountering this problem the past couple of weeks and from what I've seen it gets progressively worse the longer you stay logged in, so it could very well be a sync issue. Last friday I logged on to rank up my archer, and was having no issues with timers, but the very next day I noticed my raging strike timer was no longer 30 seconds, but 28 seconds, however when it lit up I had to wait a few more seconds to actually use the ability again. Last night, having left the client on for about 4 days, my raging strike timer (once used) was down to 19 seconds, however I still needed to wait the additional 11 seconds before being able to use it. I shut the game down, logged back in, timers are back where they should be.
yeah you have to restart ffxiv to fix it
This actually fixed it for me.