What's causing this

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The stabilization in FCP is likely responsible for most of what you are seeing. Some of it may be focus related but in my experience youll get that odd defocused look from motion blur in the stabilized video frames.
I will try the footage both ways today that I shot earlier to see how it does. Do you normally not run any type of software stabilization/
 
I will try the footage both ways today that I shot earlier to see how it does. Do you normally not run any type of software stabilization/
Only to correct for the camera kind of wandering around. It wont do much to help with jerky footage. If the frame makes sudden jerky movements you will likely have motion blur which after its stabilized looks exactly like focus hunting. I bet if you watched your original footage and the stabilized version most of the times it seemed to go out of focus the camera had a quick jerk.
 
Don't worry too much about using TC's -- good tracking in video mostly depends on sufficient contrast and subject isolation. I've posted this example clip before but will do it again -- this was captured with the A1+200-600+2xTC (1200mm) stopped down to @f16. The A1 lost focus a couple of times only when I lost the bird in AF area of the frame or the ground cover became prominent...

Very nice video. Was that shot with autofocus?
 
Yes, AF. There's no option when it comes to BIF -- the DOF @1200mm is razor-thin.
Slowly but surely I'm getting it figured out. 95% of my video footage has been drone footage which does away with nearly all the issues with mirrorless/handheld cameras. I do think I'll focus more on using manual focus for more static subjects. I feel like the A7RV tracks better in video than the A1 as well and the subject detection seems to really make a difference.
 
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