Something different has happened with the last two sequences I have processed in LRT. Near the middle of the sequence, although the total exposures of the frames match perfectly, there is one frame transition where the sky gets darker and the landscape lighter, which appears as flicker even though the total exposure of the frames match. Defining the sky and then deflicker makes the landscape flicker twice as bad. Defining the landscape and applying deflicker makes the sky flicker twice as bad. This is something the just started happening after never having this problem before. Any ideas or thoughts?

I just realized that both sequences in question the camera was panning up, from mostly landscape to mostly sky.

Hard to say - sounds like a change in contrast. Might due to some thing changing in the light in that frame. This might get more noticeable, if you edit very intensively in Lightroom, something like I've explained here: http://forum.lrtimelapse.com/Thread-what...htroom-acr

Hi, James. Did you solve this issue? It is likely that I am experiencing same issue.

I'd try to redo the sequence with as little Lightroom editing as possible and see if this goes away. Lightroom calculates the behavior of some tools based on the contents of the images. It does this even for contents that are outside the crop. For example if you have a timelapse, where you have a dark car passing in one frame and you find a crop where this car is outside the crop, Lightroom will still apply some "non linear" tools like clarity, dehaze, whites, blacks depending on the content and make that frame appear differently, even if the disturbing car is outside the frame. That's a really weird behavior in Lightroom, but unfortunately we have to deal with it.
The solution is to avoid editing sequences that have those appearances too much and only do the important things like Holy Grail Leveling, Deflicker, Whitebalance in LR/LRT - the final contrast editing should then be done in the video editor after rendering.