I've never seen that in any of my tests, but that doesn't mean it isn't a bug. Have you deleted anything in the DB (as opposed to doing it in the Manager)?
Have you changed the names of any of the TVs?
Have you changed the template used by any resources?
discuss.answer
TV names have not changed (though I was sure that was the problem). No (recent) changes to the template/resources relationship or db deletions either (see below).
When I looked at the 'modx_site_tmplvar_contentvalues' table I saw dozens of rows belonging to previously deleted member-created resources, and for whatever reason that's where the incorrect content was coming from. Since this project is still in development I decided to manually delete all the rows, then delete all member accounts and any member-created resources (all from the Mgr.). I then registered a new member and created a new resource (with NP) and it all seems to be back to normal, the front-end and Manager TV values match exactly.
Todd
The modTemplateVarTemplate entries are supposed to be deleted when you delete the resource or the TV. I'm not sure why they weren't, but I don't think it has anything to do with NP -- all of it's TVs and Resources are created with the resource/create processor.