Have you changed the order of a track with this project?
There is a known bug when changing the order of a track.
Do you have other filters on any of the other clips than the black one on V3?
As far as your description, I tried to duplicate the issue, and only have applied 2 filters, Opacity to the black clip on V3 (Keyframed 0 to 100), and Chroma Key Simple on V4.