mod1.py

class Base:
    pass

if __name__ == '__main__':
    from mod2 import Derived
    print("Derived:", Derived)
    print("Derived.__bases__:", Derived.__bases__)
    print("Base:", Base)
    print("issubclass(Derived, Base):", issubclass(Derived, Base))

mod2.py

from mod1 import Base

class Derived(Base):
    pass

running.txt

agrif@nara ~/devel/other/hesperus-realistic/bug $ python -m mod1
Derived: <class 'mod2.Derived'>
Derived.__bases__: (<class 'mod1.Base'>,)
Base: <class '__main__.Base'>
issubclass(Derived, Base): False
agrif@nara ~/devel/other/hesperus-realistic/bug $ python --version
Python 3.3.2