The same problem occurs without a manifest template: you can have options or imports in setup.py that will change the MANIFEST file. 

For example : if setup() has:

  packages=['foo']

And if you add a subpackage "bar" in "foo" with some modules, with an existing MANIFEST, they won't be added.

IOW, the MANIFEST file should be recalculated *everytime*. I am going to remove all the "don't rebuilt MANIFEST" code in Distutils *and* Distutils2.