Difference in images after edit

Question

I was shooting timelapse, pictures shot with the same settings and with three seconds interval.
The .raw images looked and was just the same. After edit, some differences occurred. If you look at the bottom images. That's the way it should be. But the top image appeared to have lost some contrast. This happened to some images. Why did this happen?
If you look more closely. On top of the images you can see some black unwanted object. It's my window. I couldn't open it any more, and the wind kept moving the frame of the window in my view. Also my floor is a bit uneven so every time I went to check on my camera the camera tilted. I just stabilize and crop the images. But, the low contrast-problem on the top images seem to occur on the images when I stepped in front of the camera and created some movement. Still, .raw-image looked just the same. It was after edit this happened. Shot in manual mode.

Answer 1

It is my analysis that the black window frame at the top is causing the difference in brightness between the two raw images even though exactly the same camera exposure and Lightroom adjustments were used.
Lightroom toning adjustments are somewhat non-linear, meaning the image content dictates how much things become lighter and darker.  This is especially true of Whites, Highlights, Shadows, Blacks and Clarity.
In this situation the window frame at the top is a dark object darker than anything in the rest of the image, so it keeps the darks from becomes as dark as if it wasn't there.
Effectively it means you cannot use the Shadows, Blacks or Clarity with this sequence of raw images because of the varying amounts of black.  The amount of cloud shadowing on the image will also have some effect, especially for Clarity, but less so compared to very dark or very bright pixels.
For this sequence of images, the best thing to do is probably FIRST crop all the images the same so that no extraneous window frame is showing on any of them, THEN synchronize your white-balance and other non-color and non-tone-related adjustments--noise-reductions, sharpening, and THEN do an Export of all the frames to 16-bit TIFs with a ProPhotoRGB color profile.  Reimport these into LR and do your toning and color adjustments.  It is not enough to crop the raw images, because the toning adjustments always look at all the pixels including those outside the crop box, not just the visible pixels.
RAWs and TIFs don't act exactly the same as far as toning and colors but you might start with the raw toning and color settings synchronized to all the TIFs and see if there need to be any other adjustments.  Here is an example of my doing this where the first column of images are your two raw files with identical settings, and the second column being two cropped TIFs with the same adjustments.  You will notice that the hill, especially the bottom-right corner, is a different brightness between the two raws but the same brightness between the two TIFs.
I don't know what would cause the difference in color in the night shots, above, unless it is a slow drift caused by the camera sensor warming up with use and the high-ISO noise increasing and affecting some colors more than others.  If you're seeing a slow drift then this is likely the situation.  If you're seeing the color randomly change back and forth between different frames, then it is likely something else that I don't have a theory for without more information.  Usually a random fluctuation of color among various images happens indoors with fluorescent lighting because the color and brightness changing with the A/C 50Hz or 60Hz frequency.  Nikon cameras for a few years, and the newest Canons, will detect this fluctuation and time the shutter opening with the peak brightness so every shot of a burst will look similar.