(searched this thread but not seen this mentioned)
I've been shooting with dual ISO for many months on my 6D. Normally not noticed any issues. This weekend I went out and shot a bunch of images, using ISO 100/1600, with my camera mounted on top of a pole and remotely triggered using Pocket Wizards. When I reviewed the photos later, I noticed some did not shoot as dual ISO.
They seemed to perhaps be related to waking the camera up after a couple of minutes, and the first burst is capturing in 'normal' mode, before it switches on dual ISO. I missed a few shots (or more properly, I got them but they're shot a couple of stops under) which is a bit of a shame but hey…but as I've never come across this inconsistency before I wanted to post it here in case this is known.
My guess is that the half-press to wake is enough to get the camera ready for shooting, but there's some kind of lag/delay before a command kicks in to enable dual ISO for the remainder of the burst (or for a second burst). Camera was set to continuous shoot mode.
FYI Build was magiclantern-Nightly.2015May03.6D113