Sounds like your suffering from latency issues overall. There are times it appears to be spot on and you can easily avoid it but after the 2nd or 3rd run you can suffer from it and not even realize it.

Just to be clear though sometimes it's not connection issues, sometimes it can be latency issues with your video card being slow at drawing the animations and showing in the log. Case in point I had some serious issues with Ifrit's Eruptions for some time until I lowered some of the video settings. You might try and lower them and see if you have any improvements.