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Force.com -> Save to Server is additive; doesn't overwrite!

I've been looking at the Force.com IDE add-on for Eclipse...


If I make a change to a pick list value within the IDE and then do Force.com -> Save to Server, the modified pick list value is then ADDED as an additional pick list item. 


This is not what I'm wanting to do, I want the Save to Server to replace what's on the server.


Am I doing something wrong?