Interesting, and I do not notice anything wrong in your statements.
Can you post a few screen-caps?
First, a screen-cap of your Timeline, with the various Clips showing, would be good.
I would also post a screen-cap of the GIF and the Video (a Freeze Frame from it).
Then a screen-cap of the Effects Control Panel, with your applied Keyframes.
There might be a clue in there.
Here is more detail and screen captures.
I have 3 minutes of video. It contains a person making a speech. During parts of the speech I want to reveal a graphic image that will be discussed. The speech will begin with the speaker full screen. Half way in, the speaker will shrink down to 45% in the lower left corner of the screen. While the animation occurs (the shrink, move and cropping) it will reveal the graphic below. The graphic will take up the full screen with the speaker at 45%.
I put the video in Video 2 and the graphic, a GIF image in Video 1. The scene begins with the speaker talking at full screen. After a minute, I animate the move of the speaker using Motion: Scale and Position and Effect: Crop changing Top, Bottom, Left and Right sides. The animation occurs over approximately 8 seconds.
I am manually adding keyframes at the start and end of the animation. I set the ending state of the video image in the end keyframes. The interpolation between these start and end keyframes should be managing the animation.
At the beginning and end of the animation – usually 1-3 frames from the start and 1-3 frames from the end, where the change has barely begun or almost ended, I get these problems. On some frames, the video (in Video 2) completely disappears only showing the Video 1 GIF image below. On other frames, the video image turns black with horizontal red bands half way across.
I’ve tried deleting all start and end keyframes and moving the start and end earlier or later to see if I can fix this, but the problem continues to show up in these new locations.
I have added a few screen shots.
1:32:15 is the start of the animation change and 1:40:22 is the end of increasing from the mini video speaker to full size (on top of the GIF).
At 1:40:16 the video image completely disappears only showing the GIF below.
At 1:40:17 its back and slowly increases in size through the interpolation until it is full size at 1:40:22.
Let me know if you need anything else.