Just to rule it out... has the system gone through a full shutdown and restart cycle since the update. Not a hibernation cycle, but an actual shutdown. It is possible some files are pulling from cached versions and not the updated ones.

Also, are your browser(s) and their technologies (flash, .net, etc.) up to date. Along that same note, have you updated the rules in your security software to recognize the new version of the executables for FFXIV?

Just want to get those off the table, as they are some of the common culprits.