https://answers.atlassian.com/questions/168110/gitflow-finish-feature-with-rebase-doesn-t-work-win

This happens whether there are conflicts or not. I hadn't spotted this because my embedded git version had a symlink laying around which let 'git flow' resolve - in fact that can't work because we avoid having to alter the user's Git install by running the git-flow script in-place. We will probably need to alter the git-flow script to resolve this, even though we deliberately try to avoid that to ensure compatibility with command-line installs.