I have been experiencing this problem relentlessly and for some reason it just starting happening last month... Have I clicked something obscure?!
When I chroma key some footage everything applies as normal. Then I try to render the clip as normal and when it's rendered the green re-appears. If I stop the render half way through the section that has rendered appears green and the section that hasn't appears rendered! If I render out the whole clip, as I mentioned, the clip is un-rendered and GREEN!!!
This is driving me INSANE. Defying all logic and 8 years of chroma key experience... sigh... Please help!
Final Cut Pro 7 - Chroma Key. I have magically sorted the issue by using Colur Key and dragging colour wheel to Chroma Green, keying the green out and, hey presto... Bizarre. Still not enlightened as to why the standard chroma isn't working as it has done for the last God knows how many years...