Pycharm (Python IDE) doesn't auto complete Django modules
I had exactly the same issue and couldn't find a definitive answer. Just invalidating caches didn't work for me. The problem lies in the fact that, at some point, __init__.py files got registered as text files and messed up the indexing. I worked out this fix:

Preferences > File Types > Text Files.
Remove __init__.py from the list of registered patterns. Apply.
Wait for your indexes to re-build.
(If it's still not working) File > Invalidate caches & restart.
My Python IDE (pycharm) has stopped auto completing my modules (suggestions). I get unresolved references after every django module I try to import so:
from django - works, however soon as I add a 'dot' it fails so from django.db import models gives me unresolved errors...
The ackward thing is after compiling references DO work.
I discovered that all my __init__.py files (everywhere) no longer are marked with python icon and are now notepad icons. Also opening init files in my interpreter gives non-color marked up text (no syntax highlighting). So I think Python doens't recognizes these files.
My python interpreter is python 2.6.1 with Django 1.2.4 and my django is installed under:
/Lib/python/2.6/site-packages (full directories, not egg)
When I unfold sitepackages from external libraries within the IDE I do see colored mark up for all .py files EXCEPT __init__.py files. Hence thats where the issue lives.
(I have found posts on google for similar problems but no answers...)