My PyCharm 5.0.1 installation does not resolve references to any builtin modules or methods:
As you can see, I have installed python over cygwin.
I alr
I use Windows 10 x64, Python 3.5.1 and PyCharm Community Edition 2016.1.4
I have the same problem and sovled it by runnig PyCharm in admin mode (it is required only once).