I've ran into this scenario a lot it seems. I'm not sure if it's an issue with SharePoint Designer, or SharePoint itself, but the following seems to occur often:
I create a Workflow in SharePoint Designer, and when I save it, it's good to go, and works as expected. However, when opening it later for edits in SPD, I can make changes to the workflow, very large ones, and save it, and on the SharePoint site, it shows as a new version of this workflow, but never reflects the new changes I made to it.
For instance, I created a simple one to test, simply an email gets sent to me when a new item is created in a list. Works fine. However, when I add an item lookup in the body of the email, save the workflow again, and create a new item in my list, I still get a blank email, not the new item lookup in the body of the email as expected.
Is there some kind of timer with SharePoint updating workflows? Am I missing something here?