Interpreter thinks 2 declarations of the same class are different

Basically I have a project set up like so:

<container-folder>
        |- <folder_1>
               |- <extra_folder>
               |        |- source.py
               |
               |- main.py

And in main.py I declare a class like so:

class ClassOne:
    pass

and in another method in main.py I have the following code:

result = source_function()
if not isinstance(result, ClassOne):
    print "failed!"

In source.py, I define

import container-folder.folder_1.main
...
def source_function():
    return main.ClassOne()

However, I still get "failed!" printed out. When examining in the debugger, I got a bit of an odd surprise:

result was marked as type container-folder.folder_1.main.ClassOne, and ClassOne has the signature main.ClassOne. Why are these two not considered equal?

I also noted that if I changed the code to the following, using its fully-qualified class name:

if not isinstance(result, container-folder.folder_1.main.ClassOne):

I get the expected success.