First, please read this post and give us ALL the information requested there. At the moment we know nothing about your computer nor even the version and variant of Movie Edit Pro you are using!
Then, can you go step by step through the procedure you are using when using the Chroma Key effect? Although this should not be affecting the outcome it is worth us being able to "visualise" your workflow.
However, there have been other reports in the forum of problems with Chroma Key and specifically the use of Green. One such post, here, albeit applying there to Video Pro X, is well worth a read, I think.