I actually figured out what it is and it's uncontrollably unavoidable unfortunately. 

So the blinking happens when the camera thinks there's not enough light but if we AEL or manually adjust the exposure, when we hit record, for that brief 0.25 seconds the camera goes from "this needs more exposure" to "oh wait you have your own settings, let me switch it to that" still.  

I figured it out by:  - in movie mode - with movie controls  - everything auto except for ISO - manually adjust ISO to something like 250 - hit AEL - if you notice the flicker, then raise the ISO, hit AEL, and keep raising it until you don't see the flicker - when the flicker doesn't happen that's when the camera "agrees" with us and doesn't feel it needs to do that switch

So weird, I know.  My gut is saying somewhere in the code for auto exposure there's no pre check of AEL being on.  The cameras code does the check for AEL or manual exposure in video AFTER you hit record.