This is a known issue and is fixed in the pylint source (https://bitbucket.org/logilab/pylint/issue/55/) but not the PyPI module. I have updated pylint from source and it works correctly in a terminal.

The version that python-mode uses still has this bug. How would I update python-mode to the latest version of pylint or tell it use the version of pylint that I have already installed?

Thanks.

e: as the issue seems to be related to Windows-style carriage returns, I've found that :set ff=unix will make things work.