I have found this problem very annoying after not knowing what it was and running into it several times. We finally resolved the issue after banging our heads against the wall. If you have a list with a workflow and want to save the list as a list template and save the data you will run into this issue. I even checked the setting to include this data.
What happens is when you have your new list, you try to import your original workflow. You do that because the original workflow does not appear in SharePoint. In trying to be consistent, I try to name the new workflow the same name. An error appears telling me the workflow already exists. Well, how can that be when it does not appear in the workflow list for the list you are working on? However, magically if you go to SharePoint Designer you will find the workflow under the list even though it doesn't appear in SharePoint. You will have to delete that workflow in SharePoint Designer. If you do not, you will have problems with the workflow running actions twice. We ran into emails firing twice. I believe it was because it was running the workflow twice. Be careful of this issue.
