After I applied the auto-transition on my photos and reread the metadata in Lightroom, the keyframes I edited are brighter than the non-keyframes. When I read the metadata in after the auto transition I make sure I selected all photos, including the keyframes, what am I doing wrong?

I'm using Lightroom 4 and Lrtimelapse 2.

You might have used some tools in Lightroom that are not supported, check out this thread:
http://forum.lrtimelapse.com/Thread-what...htroom-acr