Well - I would expect the IDs to be different between the list and library - each list (a library is a type of a list) in SharePoint will have unique IDs for that list, starting at 1 and autoincrementing by 1 from there. These IDs never get re-used, so if you delete item ID of 2 from a list, you'll never have another one in that list.
I don't understand this:
Christy Rohmer:then the workflow rewrites the form and leaves everything blank.
The workflow is creating and submitting the XML? Why is it sometimes succeeding and sometimes not? If you look at the XML (open it in a text editor), you can see the nodes do not have values?
Can the end user open and edit these forms that are being created by the workflow? I ask because I'm curious about how you intend to handle a scenario where a user edits the XML that the workflow is creating and another user changes the list item that is supposed to update this XML....