For the Nikon cameras that can perform rear curtain sync, one needs to
be using the shooting mode of P (Auto Multi Program), S (Shutter
Priority Auto), A (Aperture Priority Auto, or M (Manual).

A quick check of the 5D manual discloses you need to use the P mode
and not the full auto mode.

wrote:
I just got a 5D and, so far, I love the camera, but I can't get the
flash to fire before the shutter closes. I did set the Custom function
#15 to "2nd Curtain sync", but it doesn't do the trick. Thinking it
could be a problem with the flash, I asked my friend to try it on his
Nikon D200 and it works fine. What am I doing wrong?