Let's see if I understand:

You said: "If I re-enter a name it appears in both places again."

Does that mean: You have the name in your file twice and it appears in your index twice?

Or, does it mean: You have the name in your file once (in the index once) and it appears in some report twice?

I am pretty sure you have a cousin marriage that is causing your situation - and FTM is operating as it is designed. FTM does not remove duplicate branches from cousin marriages in a descendant chart or report.