How are you processing the images before compiling them into a vid?
Are you shooting raws?
As Rohan said, it could be a white balance issue, especially if you shot it on auto WB. I shoot all my timelapses on auto WB but then I always apply the same white balance settings (custom WB values) to all the raws when I export them out of Lightroom before I turn them into a vid.
I used to do heaps of timelapses with my 5DmkII and ML and never had a problem (I miss ML now that I'm on a Sony
)
Doesn't look like iris flicker to me as it's not really a flicker more like something is changing at a few points throughout.