I have been experiencing a phenomena with my 5D Mark iii and wanted to see if anyone else have had this issue. I have sent both my camera in as well as my flash and Canon said nothing is wrong. I shot a quick video this morning showing my issue then called canon tech support in Virginia and to my surprise this issue was being duplicated by the tech.
In a nutshell My camera is all in Manual except for the focus and I am using either my 580EX2 flash or the 600EX-RT flash on ETTL directly mounted to the hot shoe. After taking a photo (typically happens when over 800 iso) I wait for about a second or two after the green confirmation light turns off and the take another photo. The Auto focus assist light turns on, the camera locks focus and takes the photo, however the flash fails to fire. It seems to only happen when in auto focus and I manually select the ISO. If I use it in manual focus or in auto ISO select this issue does not appear.
The tech at canon has no idea why it does this because he also tried it on the 7D as well as the 70D and the flash fired each time. The issue only happens on the 5D Mark 2 and 3. It happens more often when in a dimly lit room as opposed to a bright room. Not sure if it is related, but my issues started on my Mark3 only after I updated the firmware 5 months ago or so.
Please let me know if anyone else has experienced this problem and what they did to fix it.