Usually this is cause by the init.py missing in the package. But I do have all my init.py into place. In the PyDev package explorer, packages are displayed as yellow rectangles, just like regular folders, rather than with the package icon. Why is this? I've tried clean all, build all, doesn't help.
Sounds like an issue with the indexer, or PYTHONPATH. Try Project -> Properties -> PyDev -PYTHONPATH, "add source folder"