That's pretty cool. I checked LRTimelapse on YouTube. It's pretty good. I used Premiere/AE as I already use them from work and I'm familiar with both softwares.
What were your camera setttings during the transition to dark. Did you set aperture/exp time to automatic or a set value?
Also how CPU intensive is your video encoding. I found that to do HD on my I7 I had to replace the stock CPU fan with a
water cooled H60. I peaked at 75c at 100% load with the stock cooler. The H60 keeps it down to 60c.