The final seeping shadow isn't reachable without flight (forcing you to do the adventure timeline or get a friend to call you. Secondly it is invisible once you reach its spawn point until you use another Advanced Tracker Mach II to get it to appear.
I'm thinking that there are more than three spots for the Seeping Shadow, since alts running the quest have found them in different places. Also, I have seen one spot respawn a new shadow not long after I harvested from it. So, I think you can get this finished without the flying spot.
The /loc for the Seeping Shadow (my 3rd) that can't be reached without flight is: 534.88, 67.97, 401.60. It's on top of a mushroom inside Murkmold Swale.
The ones that were unreachable should have been moved on the 3rd. Check after tomorrow and see if its still occurring. That change should already be on live servers.