We believe there is a bug in the pop up view that sometimes causes this. There is however a simple workaround that can be used. Once the affected user has clicked on "Merge to PDF" do the following:
Clear the IsTemplate filter
Click the small blue Create button
Choose DOCUMENT MODULE, is one of and then the relevant module
Give your filter a name such as "X Templates" (where X will be the module)
Save the filter
You can now see the documents with that saved filter