I'm not sure what all the issues are here. 
The internal flash will only trigger one time, regardless of camera shutter burst mode. It just does not have the power to give up much, and the Ready LED has to be on.
A hot shoe speed light will trigger multiple times, regardless of Ready LED, but it has to recycle (like Geoffc said). It will attempt to trigger multiple times regardless if it is recycled yet or not, but the picture will be trash if it has not recycled. Ready LED has to be on to work right and expose properly.
In short, if you are shooting 5 frames per second, you have to use low enough power level where it can recycle in 1/5 of a second. Otherwise, it will be a problem. It has to recycle (ready led on).
I don't think there is any hard rule about how low the power has to be to be sure can recycle at X shots per second. There is a little extra overhead. Some of the flashes have a Repeating mode (self triggered many times a second), and the D800 manual has an elaborate Repeat mode chart, which says, for 5 Hz repeats for example:
8 flashes max at 1/8 power
40 flashes max at 1/32 power.
Saying, every 1/5 second can only do 1/8 power. And of course, you have to pay attention to NOT overheat it, so the chart says 8 flashes maximum. The SB-800 is not the fastest recycle, other models possibly could be slightly faster?
Try lower power levels until it works.
Fully charged NiMH batteries recycle significantly faster than alkaline or even low NiMH.
So out of curiosity, what power level and what trigger rate is being tried? With which flash? What's going on?
Auto FP mode was mentioned. If it was, that has to be bad news for repeating flash, since the maximum power level is already so low (only about 1/5 power), just to be a continuous HSS flash at maximum power. Try it in speedlight mode instead.
The internal flash will only trigger one time, regardless of camera shutter burst mode. It just does not have the power to give up much, and the Ready LED has to be on.
A hot shoe speed light will trigger multiple times, regardless of Ready LED, but it has to recycle (like Geoffc said). It will attempt to trigger multiple times regardless if it is recycled yet or not, but the picture will be trash if it has not recycled. Ready LED has to be on to work right and expose properly.
In short, if you are shooting 5 frames per second, you have to use low enough power level where it can recycle in 1/5 of a second. Otherwise, it will be a problem. It has to recycle (ready led on).
I don't think there is any hard rule about how low the power has to be to be sure can recycle at X shots per second. There is a little extra overhead. Some of the flashes have a Repeating mode (self triggered many times a second), and the D800 manual has an elaborate Repeat mode chart, which says, for 5 Hz repeats for example:
8 flashes max at 1/8 power
40 flashes max at 1/32 power.
Saying, every 1/5 second can only do 1/8 power. And of course, you have to pay attention to NOT overheat it, so the chart says 8 flashes maximum. The SB-800 is not the fastest recycle, other models possibly could be slightly faster?
Try lower power levels until it works.
Fully charged NiMH batteries recycle significantly faster than alkaline or even low NiMH.
So out of curiosity, what power level and what trigger rate is being tried? With which flash? What's going on?
Auto FP mode was mentioned. If it was, that has to be bad news for repeating flash, since the maximum power level is already so low (only about 1/5 power), just to be a continuous HSS flash at maximum power. Try it in speedlight mode instead.
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