I still have the flickering issue. I uploaded a time lapse to show the problem... The log file is also attached.
Is there a way to see if the ND filter was in or out from the EXIF data of a photo?
It looks like everything worked great until you got to IMG_1704. This image was 2 f-stops brighter than IMG_1703. Will you look at those 2 pictures and confirm that the second one is a lot brighter than the first?
As the cows walked in front of the sun, the meter reading changed by 1 f-stop. The script handled that ok, and you'll notice that the ground in front of the cows briefly gets brighter while the cows block the sun.
However, the sudden 2 f-stop change is what messed things up. Specifically, the bvdelta parameter is designed to gradually underexpose the images as it gets darker. But it doesn't take into account the ND filter. So if the ND filter suddenly went in, the script would think it got suddenly darker.
Anyway, the flickering would be explained if you pressed the <display> key right before IMG_1704, and the ND filter is about 2 f-stops. Did you press display?
I'm not sure if the ND filter state is in the EXIF. I don't think so, at least when it's set from a script or CHDK menu. But from the shutter speed while the sun was in the frame, it looks like the ND filter was IN when you started. Maybe you pressed <display> after it got dark? That won't quite work yet, but I'll add ND filter control soon.
Thanks for doing the video. Other than the end, it's a great time lapse!