I use three interpreters (Py27, Py33, Pypy) - all of them have this issue, but for different packages. For example if I type: "import gspread", the gspread is underlined with red, and the hint says: "No module named gspread". Of course all the auto-completion and hints are switched off for this module. But it actually work for current environment - I can run and debug the application. Moreover I have gspread installed for all three interpreters I have.