Timelapse opening sequence shot on 550D with Magic Lantern.

I have a 550D and I love ML. I have used ML for quite a while. I like focus peaking, audio meters and overlays. For over a year I have been working on a passion project (On Holy Ground) and now I want to add timelapse to my videos as well. After limited initial tries at home, I felt confident and I went out for a test 'in the field' and ... I messed up.

My only success was actually at the start of my field test: a 300 shot series with the intervallometer. The result of that is posted below, and I have a question about it (see below).
Then I started worrying about all the shutter clicks, so I thought the FPS override mode would be better for the life expectancy of my camera. So I went into FPS Override mode. At 1/3 exposure, my shots were overexposed (I was shooting straight in the sun), and that's when I made a mistake that would ruin the rest of the evening: in order to get correct exposure, I wanted to change the aperture, but unfortunately I turned the aperture ring of my manual lens in the wrong direction (I only found out when I got home it was at f4 instead of f16!), so my shots stayed overexposed... Then I started panicking. As far as I'm able to reconstruct, I must have turned the dial to movie mode, while in FPS Override and intervallometer mode, the result is that the camera stopped clicking (which I thought was good), but instead of recording one long movie at 3fps, it recorded a sequence of separate movies... As it got darker and colder, and I felt insecure about the outcome of all this, I soon gave up...
At home I could easily edit the timelapse sequence (see below). I also looked at the movie sequence: it was correctly exposed, but boring and too long, while there was not noticable movement of the sun in it, so I didn't use any of it.

So here is the result of my fieldtest. (jpegs heavily edited in Lightroom). Question: there is some flickering. What could be the reason?

UPDATE: The flickering, I found out after some research, is probably caused by the short exposure times of the still images (1/1600). It is advised to keep exposure under 1/100.

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