Frame in the general area, press the focus square selection button (focus squares are bright and easy to see), move the desired focus square over the point you want to focus, press the shutter button halfway and the bright focus squares dissapear and you now achieve focus and metering - take picture.
I have only tried this in manual with flash attached and turned on.
Hope this works for others that were having the same problem as me. I just could not find my selected focus square (usually center spot) as they were very dim and only remained on for a split second, lock focus and then shoot. I hope Canon will give us a fix for this in the April firmware update. I never had this problem with my 7D.
Let me know if anyone else has any other ideas. Thanks