Just bought the 800 and am using the 50 mm 1.4. I am shooting my kid indoors. Using pop-up flash and manual mode, Shutter 1/250, f5, Auto iso (between 4000-6400)> I am putting a single focus point on my son's eye. The focus point turns red and the green light in viewfinder is on and solid, yet many times the shutter won't release What's going on here?
Sounds like the OP is stating he has a solidly lit focus indicator but cant always get a shutter release. Not sure what could be happening. Maybe the shutter release delay is turned on by mistake, just guessing.
"Things are'nt always quite as cherry, as they first seem"
Your pop-up flash needs a second or two to recharge after use. When you first activate the pop-up flash a lightning bolt shows up in the lower right-hand corner of the view-finder. Right after discharge the bolt turns off. The shutter will not release again until the lightning bolt reappears. This is true whether you are in focus or release priority.
This need to re-charge has been the same on my other Nikon DSLRs as well (D7000, D700).