Choppy Animation After Export

I have created an animation consisting of three layers:

Layer One (bottom): A girl sitting at a computer tapping away at a keyboard (captured 4k 24fps)
Layer Two (middle): Computer screen recording (submitted from an outside source captured at 1080p)
Layer Three (top): Duplicated Layer Two to use for animation

Layers Two and Three were taken into Fusion and set to fill the computer screen on Layer One using Corner Positioner

Layer Three opacity is set to 0 to fade in and fill the screen a few seconds into the clip and reduce to size and fade out at the end of the clip.

All views fine on the timeline, but when I Deliver the animation is choppy. I'm exporting as an uncompressed ProRes, RGB 10-bit, 1080p at 24fps. I've set Data Levels to Full and defaults on all others. I take the .mov into Handbrake for compression to the final mp4 to post on Vimeo.

You can see the choppiness that I'm describing at about 00:00:42 and again at about 00:01:04. https://vimeo.com/389170556/52e2b044e3

NOTE: I'm compressing in Handbrake because I was having color issues exporting out of DaVinci. I'd read about Handbrake in another forum being able to help with this which it did tremendously. Maybe Handbrake is the 'choppy culprit'? Dunno.

Any suggestions?

seems that you animate graphics without motion blur, but after thre compression (1 export 2 handbrake 3 vimeo recompress) it's not clear who cause what.

It almost looks as if it's been rendered with fields - and then those fields were reversed.
Is the choppiness also in the Prores? (i.e. if you load the prores back into Fusion does it show the same issue? Because it could also be a handbrake setting in that case)

also triple check the frame rate is the same between these conversions. also try boosting the data rate in handbrake.

Thanks, everyone. Sorry, I've been out of town so I didn't get your replies until now. I'll check all of these suggestions and try them out.