Hello,
I've applied deflicker to my sequence, but no matter where I set the reference point the flicker remains.  Any ideas on how to fix?  Thanks.
   
   
   
   

Looks like as if you have applied very strong Lightroom contrast adjustments. Lightroom might introduce some contrast-flicker then, that can be very hard to remove. Generally I'd suggest to not edit so much and use a rather bigger reference area and then apply multiple deflicker passes (after the first visual deflicker, save and wait for the previews to be generated again, then use the visual deflicker again with "refine".
Here is some explanation about the Lightroom specifics with strong editing: http://lrtimelapse.com/news/use-the-new-...me-lapses/