To use workflows in a site template, you need at least the SharePoint Infrastructure Updates and also the latest build of Nintex Workflow.
Unfortunately, list templates handle workflows very badly. In our experience, it only half saves the workflow, resulting in a 'ghost' workflow on the destination list that is difficult to manage. For example, if the workflow is set to run automatically, it will run, however there will be no mention of it in the list of workflows, so you will be unable to remove it.
This is the behaviour with both SharePoint Designer created workflows and Nintex created workflows because our workflows are architecturally the same as those from SharePoint Designer.
There is also no way to export the list without the workflow.
You need to remove the workflow from the list, and then create the list template.
You can then export the workflow manually from the workflow designer and import it at the newly created destination list.
To remove a workflow from the source list (this will not delete the workflow, it will appear as a saved workflow that has not been published. However it WILL break any running instances):
1. Open the library or list the workflow exists on
2. Choose the ‘Settings’ menu and select ‘Document Library Settings’ / ‘List Settings’
3. Choose ‘Workflow settings’ under the ‘Permissions and Management’ group
4. You will see a list of all the previously published versions of the workflow. Select ‘Remove a workflow’ down the bottom.
5. Select the Remove option next to all Nintex workflows and versions.
All internal SharePoint references between list and workflow have now been removed and the list template can be safely created. If you choose the library settings, and ‘Manage Workflows’, you will see all the workflows are not listed under the not published category. They can be re enabled by publishing them again.
When you create the list on the destination site, those workflows will not appear as saved. You will need to export the workflows manually and import them at the destination.