It's not very intuitive but the Time Lapse app overrides whatever the camera dials are set to. You have to actually go to the app settings for the timelapse mode that you use and under AE you have to select something other than Lock. In your case, it would seem, from your description that the AE value was locked rather than set to tracking. Completely unintuitive I know but basically just realize that it makes absolutely no difference what you have your camera settings set to external to the app, every single thing must be controlled within the app.