I have the same issue. You can find my thread here:
http://forum.square-enix.com/ffxiv/t...FFXIV-affected
This began happening for me after I switched ISPs. Oh, it's so easy to say it's my ISP's fault, but the issue begins occuring on NTT's nodes. On my old ISP, I was taking a completely different (and apparently less congested) route through NTT's nodes. I was even able to run traceroutes at the same exact time with both ISPs (old one wasn't deactivated yet), showing that one route was fine, but the other wasn't. So if you're lucky enough to actually have a choice, switching ISPs is the only solution I can come up with, besides maybe using a VPN.
