Ok here we go again. I've had the same issue now for about 2 months with no resolution in site . Have made multiple posts and was hopeful that the new patch would finally resolve the issue. Here is a link to my original post.
http://forum.square-enix.com/ffxiv/t...62#post1324562.

I still am unable to progress in the main story . The quest "Shadow of darkness" is not available after completing "Back from the woods" I have gone so far as to upgrading my pc in order to buy the PC version in hopes that the issue was related to a PS3 bug, but alas it seems it is universal . Starting over at this point would be a game breaker as I'm already at level 50. I've taken the liberty of posting several other people who have had this issue at the bottom . If the quest "back from the wood" could be reset I could do it over. this would most likely resolve the issue. I've made several calls to square , sent countless emails and there is no resolution in sight . It looks like counter measures where added to the game in the new patch but no fix was implemented to resolve issues where people have already ran into the bug. Any response would be appreciated.

http://forum.square-enix.com/ffxiv/t...od#post1404818

http://forum.square-enix.com/ffxiv/t...od#post1398193

http://forum.square-enix.com/ffxiv/t...es#post1404818

http://forum.square-enix.com/ffxiv/t...-from-the-Wood

http://forum.square-enix.com/ffxiv/t...od#post1287509

http://forum.square-enix.com/ffxiv/t...od#post1251297