Nicely done! The video looks great. I have not downloaded and opened the zip file, but I suspect the issue is a speed issue or an optical illusion. Try slowing down the rotation speed of the driving gear and see if that makes a difference.
100% it's a visual anomaly. How many revolutions do the gears appear to turn? During the whole video they look like they're only turning about 1/4 to 1/3 of a turn. However, your shafts make many revolutions, as evidenced by the number of times the thread start passes by. Also, examine the hex cut into the center of the middle gear. It should turn just as smoothly as the rest of the gear, but instead it jumps all over the place, out of sync with the teeth.
I went through this several years ago with a video that had so many moving parts I had to write an excel formula to figure out the optimum frame. It’s the same problem movie makers had with black and white western movies where wagon wheels appeared to rotate backward.
To look smooth and appear to rotate in the right direction:
-The gears must rotate < 360 / 14t / 2 per frame
-The hex. must rotate < 360 / 6 / 2 per frame
-The threaded leadscrew must rotate < 360 / 1 lead / 2 per frame
So, each frame when gears, hex. and thread are rotating must satisfy all the above. The more moving parts you have with different teeth/flats/threads, the more frames you'll need. Linear frame movement doesn't have this limitation.
To expand a little further, these deg. values would work also. For lots of moving parts, figuring out the optimum rotation angle per frame with the technique below is tedious but once determined it can greatly reduce the number of frames required. That's where excel helps.
Hex – 0 < 30 deg
> 60 < 90 deg
> 120 < 150 deg
> 180 < 210 deg
Gear – Same concept as shown with hex. above.
Thread – Same concept as shown with hex. above.