Custom LabVIEW projects

I am trying to create a new template to be used with LabVIEW 2013 Create Project wizard. I have followed the tutorial 'Using Custom Templates and Sample Projects to Develop LabVIEW Projects' but still seem to be having issues.
I am pretty sure it is something really simple that I am doing wrong but can't seem to find the issue.
I have placed the template project in LabVIEW Data/ProjectTemplates/Source and the xml in LabVIEW Data/ProjectsTemplates/MetaData.
When I create a new project using the wizard, the project gets created and runs perfectly the first time.
Then when I open it a second time, there are a load of conflicts that all of a sudden exist where some of the vi's are linked to the template project.
I can go and resolve all the conflicts and then the project works but there must be something that I am doing wrong.
I will be grateful for any help getting this sorted. I have attached the conflicts and my xml file (I have changed the extension of the xml file to attach it).
Thanks,
Greg
Certified LabVIEW Developer
Solved!
Go to Solution.
Attachments:
Conflicts.png ‏95 KB
TemplateMetaData.txt ‏1 KB

I am trying to do the same thing, and am curious -- is there any way to have auto-populating folders in the template that will point to the correct folder after the wizard runs?  
I use auto-populate in all of my projects, I had assumed that auto-populating folders used relative paths instead of absolute paths.  Since an autopopulate folder in a template points to the template folder after the wizard creates the new folder structure it would appear that auto-populating folders use absolute paths and there is then no way to do what I'd like...  Any thougths?
For now it appears that I need to manually duplicate my basic folder structure in the template project, then after the wizard runs I'll manually convert the folders to auto-populating.

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