If you need to have more than one workflow for a particular list/library, DO NOT copy a SPD workflow and paste back into the same library.
What happens is that even if you change all of the properties of the files (names, etc.), there is still a hidden property that SharePoint likes to hold on to and uses to identify the workflow. Think of it as an ID.
Basically, you will have two different workflows with the same ID. When you publish one of these to a list/library, everything works fine. When you go to publish the second one, everything seems fine but after close evaluation, you will notice that the first workflow that you published is no longer attached to the list/library.
Moral of the story, don’t be lazy. Create a new workflow even if all of the information is the same.