I had a problem on a shoot the other day with my Pocket Wizard FlexTT5 on my Nikon D3S with a Nikon 70-200MM F2.8 with VR II. Even though I saw a flash of light come out of my flash, the photo was almost completely dark. I called the engineering support staff at Pocket Wizard and he said that they have a problem syncing the TT5 when VR is on. The problem also occoured with my Nikon 105MM F2.8 VR lens. When I switched to a non-VR lens the problem went away.
THE FIX - while in manual mode, switch your shutter speed to 1/200 and take a photo and then you can change the shutter speed to whatever you want. For some reason they can get in sync at 1/200 and once they do that they are good to go.