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Well I just shot all evening and did not notice this with the June 17th build.
Only difference?  Instead of doing the auto-ISO / then hit AEL before recording, I just used ISO 100.  No idea, but I just used my variable ND filter to adjust exposure and all was well.

Random theory - normally when taking photos, pressing AEL will lock the exposure but only for a certain number of seconds (while the * is showing) before it times out. Perhaps that timeout is still being applied while the RAW video is being shot?

The new RAW histogram is fantastic, it cuts a lot of guesswork out of getting the correct exposure and I will be using this feature heavily. Thank you! So far I've played around with it on my 5D3 and it seems to be working well. I especially like that it appears over the preview even if I'm viewing it fullsize. Up until now I've always found it frustrating that I couldn't see the (standard) histogram unless the image was just a small thumbnail in the top left. I would have to cycle through the 4 different display modes to review both the composition and the exposure.

Prior to now I've always used an "Image Review" setting of 2 seconds but now I'm finding 4 secs isn't enough either and I might need to set it to "hold" instead so I can take a good look at the raw histogram - it's much smaller than the standard histogram and takes my brain (and eyes!) a while to register what it says. Perhaps I'll get used to that in time though...

Something I noticed while reviewing a just-taken image. If I cycle to a different display mode via the "info" button, the RAW histogram immediately disappears Would it be difficult to keep it there for as long as the image was being reviewed, regardless of how many times info was pressed?

Further to that, I know it's a long shot (and non-trivial) but would it be possible to save the underlying histogram data that goes with each image (perhaps in a sidecar file, or a central DB)? Being able to see the raw histograms when reviewing older photos too would be incredible. If such a thing was possible then the code could be extended to store other Magic Lantern metadata too, opening up all sorts of interesting possibilities.

The one thing I can't quite figure out is that it's not clear to me what the numbers inside the R/G/B circles mean. I know the circles indicate a blown channel, is it a case of the higher the number the larger the area that is blown out?

Lastly, something that has been in the back of my mind for a while is for a way to get the camera to automatically calculate the best ETTR settings for you and take a shot based on that. There's an interesting article about exactly that here too: http://www.luminous-landscape.com/tutorials/optimizing_exposure.shtml (read the section titled "Welcome to the 21st Century"). Would it be possible for ML to take a test shot then calculate from the RAW histogram what the optimal ETTR exposure would be then immediately take another shot using the adjusted values? I can see this isn't always going to be easy, eg presumably there would need to be a threshold of sensels that were allowed to over-expose, and if the test shot was already beyond that then it might take a couple of iterations to find the correct lower exposure.