I was having the same problem, and couldn't find a fix. It was also screwing up certain effects, particularly warp stabilizer every time I rendered or exported. Finally, I tried changing the renderer from Mercury Playback Engine GPU Acceleration (Open CL) to Mercury Playback Engine Software Only, and it worked like a charm. Go to File -> Project Settings -> General and select the renderer from the dropdown menu. Make sure to also change the renderer when you export. Using Adobe Media Encoder, be sure to select "Mercury Playback Engine Software Only" in the dropdown menu next to "Renderer" before you export. This has completely eliminated the problem for me.
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