I am having a problem sometimes with my HDR recording two dark or light frames in a row. I thought at first that it was my bitrate settings since I did set them higher and it seemed to go away for a bit when I lowered it to the default 1.0.

However, I shot some HDR footage yesterday of a house and many of the shots have this problem. I admit that I am doing a pretty big leap in my ISO selection from 100 to 3200. Is there anything I should consider apart from my ISO settings, or should I just drop it to 1600?

I'd recommend 160 and 1250. Those are known "clean" ISOs on the 5D2 and give three stops of difference. If you want more, try 100 and 1250 or 50 and 1250, if 50 ISO is available. That would give four stops of difference. 100 to 3200 is five stops, but 3200 isn't very clean.

How do you capture HDR footage with the mkii? Can you supply some tips or links?

Its done with the "christmas version" of Magic Latern Unified.
The mkii exposes 2 alternating frames of video at different exposures which is split and combined in post.

It was discussed in this thread;

http://www.dvinfo.net/forum/canon-eos-5d-mk-ii-hd/503813-5d-hdr-video-magic-lantern-beta.html

Awesome, thanks for the link!

Not sure about the 5D MkII, but there is the ability to shoot 720P 60 on the T2i's, i have my workflow figured out now. 2 short clips done in HDR mode below.

HDR test - 3 EV NO AUDIO - YouTube

Actually, I discovered that when I am shooting with extreme ISOs then I need to set my bit rate around .8X. That seems to be the sweet spot. That's with a pretty fast card also.

Any idea when the official release of this ML firmware will be released? It would be interesting to see what gets improved upon from the beta.