I'm using a Nikon D800E with my 24-70 f/2.8 lens. The problem happens in low-light situations using a YN-685N and YN-622N-TX. I shoot at f/5.6 and pics aren't that sharp, but when I use my SB-910 it's all good even on f/2.8. The situation is a little better at f/8 but it's too much for me. I am using YN's AF-assist red grid and I always get focus confirmation. Anyone had a similar issue?
This is probably motion blur, your shutter speed is too long. Try opening it to F2.8. It is very strange that it gets better at F8 though, could it be a lucky shot?