I have been having quite a bit of problems trying to smooth out light changes. As seen in the youtube video there are fluctuations in the brightness. I've manually corrected match total exposures but there is still a flicker between each exposure change.

http://www.youtube.com/watch?v=NZoJwJsssoY

What do you think? I feel like a must be missing something simple here.

Did you use the holy grail workflow? Your sequence gets brighter as the sun disappears, you should rotate the exposure curve to the right to avoid that.
Check my Holy Grail tutorial: http://lrtimelapse.com/tutorial

Even if you do the automatic matching (either via MTE or via the HG-Wizard) - you might have to fine tune the adjustments between the 2*/3* images in lightroom manually. After that re-apply the Auto-Transition-Special (HG-Workflow-Tab) for the 2*/3* keyframes.