PyCharm ignoring interpreter paths

I'm using PyCharm 4 on OSX. I have a system-wide PYTHONPATH environment variable that defines a few directories where I keep local libraries.
These directories correctly show up in the interpreter paths. However when I run any script depending on these libraries I get a: "ImportError: No module found". If I run the same command from the terminal everything works fine.

Interestingly, in the "External Libraries", my local libraries appear in RED

Glad if anyone can shed some light on this

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