The white balance on video shots was way off, while stills were fine. I assumed they would be the same, unless a custom WB was done for video?

I reset the camera to factory settings to fix it, but am still confused. Which WB settings are different for video and stills?

Did you check the picture profile for both stills and video.
My pictures didn't matchup with the same settings for both stills and video. then I realized that I had different picture profiles set. When I set both to be exactly the same, picture profile and exposure settings then the picture was identical.

So as usual it was user error on my end.
Check to make sure that all of your settings are identical.