Here's a sequence I took today. Everything was in manual mode as far as I could tell. The wind was blowing super hard but there was still a lot of flicker. I couldn't correct it in LRtimelapse.

[Video: http://vimeo.com/72164377]

[Image: http://i.imgur.com/JmgjvbL.jpg]

[Image: http://i.imgur.com/JmgjvbL.jpg]

Your reference area could be a bit top of your current one.

Have you tried 2nd pass for deflickering your sequence? You have a small exposure jump in your sequence you might as well treat it like a holy grail key frame and try to do deflicker on 2nd pass.