I know exactly what you are talking about when the timers of skills and buffs are very out of sync to what they should be. The other day while in the rank 50 raid, all my skill timers and buff timers were 5-20 seconds off the correct times which even effected my cut scenes start and end times.

As the eye trap cut scene was being viewed by me, my entire party had nearly finished viewing it and began to move forward by the time I was finished. My skill timers for Light Shot would never display as grey and not ready when they actually were just used and waiting for cool downs. By the time the ogre cut scene was nearly done for me, my party had already engaged and were moving around to dodge the ghosts because for some reason my events times and skill times were all off sync with the game.

I wouldn't contribute this to lag because the game runs perfectly normal through it but just delayed from everyone else for some reason. I think the server is having some issues with syncing sometimes because I've seen this happen rarely before but never as much since after the patch.