So, friend in my LS just had the same exact problem. This is how he ended up fixing it. Might work for you. In the Documents folder, under My Games, is a folder for Final Fantasy. In that folder, is a bunch of stuff. He /removed/ everything in that folder except "downloads" which contains the patch info, and placed it all in a temp folder on his desktop. When he restarted FF14, he had no problems. He moved files and folders on his desktop back into the Final Fantasy Folder. Eventually, one of the files or folders he put back caused the problem again. When he removed the folder/file again, the problem went away. I do not know which folder or file specifically caused the problem.

I don't know if this is the same issue he had; there are LOTS of things that can cause this sort of problem, from drivers, to other programs reading/writing to the HD, to leaving your torrents open. BUT, its an easy thing to test, and you don't loose anything from having tried (unless you delete the files instead of just moving them.)