A customer of us had an issue with Nintex recently. I've tried to reproduce his problem and was succesfull in doing so.
We've made a (custom) list. Mine only contains a 'Title' column. After creating the list I've added a WF to the list which starts when an item is created. All is well so far.
After the WF is published I've made a list template for the current list.
Using this list template, I've made another list. In this second list an item is created by a user. After the item is created, the WF of the original list starts. You also get the ability to see the 'Workflow History'. When checking out which WF's are associated with this second list, you're getting none/zero.
As you can understand, this is quite annoying.
Also, when you create a new list (using the list template) in a different site (in the same site collection) no WF is started when an item is created.
It seems like there's still a reference to the Nintex WF when you create a list, using a list template, in the same site as the original list was made.
Off-course we can think of several work-arounds for this problem at the moment.
Maybe something to fix in an upcomming release, if you consider this as a bug off-course, which I think it is.
If you like I can add some pictures, but I think you'll be able to reproduce the scenario quite easily.
Software used is: MOSS 2007 SP2, Nintex WF 11003