Recently i encountered with a major problem. I created a Workflow using a SharePoint designer and publish it. But when i did some changes and publish it is publishing and SharePoint also showing it as a latest version by putting existing one as a previous version. But the functionality remain the same. It took many days to identify actually workflow is not publishing to the server, it will publish same old workflow though i modify it.
SharePoint Designer cache workflow activities in the local user folder. thus it is actually publishing the cached workflow but not the original one.
so use following steps to clear the designer cache.
Go to C:\Users\username
and then go to \AppData\Local\Microsoft\WebsiteCache (AppData is a hidden folder so you can use the explorer to access the folder)
and Delete the cache which named in your site name.