You've mentioned a few things that hint at the idea that you're not actually taking photos in a nicely lit area.
If we exclude the flash for the moment... the camera has an auto-focus system but it needs enough light to focus. In wont focus in dimly lit areas.
So one question (I do realize this is all about flash, but there are a number of things that have to work correctly in order to get the shot so I'm trying to rule things out... bit by bit) if you are outside in the middle of the day and not using the flash... will the camera focus and take the shot?
If 'yes' - great. If 'no' - then you have a different issue (usually if a camera can take a photo on manual-focus but cannot take a photo in auto-focus mode then it usually points to a problem with the auto-focus motors on the lens.)
Having ruled out the focus system... there is the question of the flash system.
You might want to use a flash specifically because the lighting is poor... but the camera still has to focus before it takes a shot and it can't do that without enough light. So it's a bit of a catch 22 in that the flash would provide the light, but you'd get a blurry shot if the camera didn't focus first and it can't do that without the light.
To solve this problem, the camera has the ability to fire a rapid pulse of flash to create about a second (maybe it's only 1/2 sec) worth of light to allow for focus. This is referred to as the focus assist beam. By default, if the flash is enabled (either you are in full auto-mode OR if you are in any other mode you must press the button to flip open the pop-up flash) then pressing the shutter button half-way to focus will cause the flash to fire very rapidly (you'll probably hear a buzzing noise as it does this -- that's normal.) If the flash is not raised, it wont do this (it only raises itself in full auto mode - all other modes only use the flash if you raised the flash). This is described on page 101 of your manual.
So the question is: When you half-press the shutter button (with flash raised) do you see the camera firing a short but very rapid burst of light from the flash?
It is possible to disable the focus assist beam (described on page 300). There's a custom function setting that allows you to disable the use of the focus assist beam.
Some external speedlights (the Canon Speedlite 430EX III-RT and the 600EX II-RT both have this ... as do several other models) have a red pattern that they emit and the camera is able to lock onto that pattern to focus your subject. This works extremely well and even in complete darkness (and it doesn't have to fire the flash to focus.)
Tim Campbell
5D III, 5D IV, 60Da
