Mr.developer: bin/develop status command shows modifications when there were none

I'm using mr.developer's bin/develop command to get a status of packages in my src/ folder.

When I run

bin/develop status

It shows that all my packages have been modified. This is not helpful since I have made no changes to any of the files. So there's no way for me to assess what has changed.

What do I need to change to make bin/develop status show a more useful message?

Can it be .pyc files or other generated files not in .gitignore?

No those are in gitignore

And git status says all is ok?

When I cd to any of my packages in src/ and run

git status 

I get the following output:

On branch master
Your branch is up-to-date with 'origin/master'.

nothing to commit, working directory clean

But when I run bin/develop status
I get the following output

  M   Products.ECAssignmentBox
  M   Products.ECQuiz

Which implies that the packages have been modified.

Then all you can do is check that you have the latest version of mr.developer and either investigate why or report a bug.

Wild, wild guess: can it have something to do with setting 'always checkout' in buildout.cfg ?

I did have this with older mr.developer versions, maybe specifically in combination with (an older) subversion, although you are using git.
Can it be that the remote url has a slight difference?