After the Python 2.5 upgrade, clean, and python-updater, the following remained in /usr/lib/python2.4: /usr/lib/python2.4/site-packages /usr/lib/python2.4/site-packages/pygtk.py /usr/lib/python2.4/site-packages/samba /usr/lib/python2.4/site-packages/samba/__init__.pyc /usr/lib/python2.4/site-packages/samba/printerdata.pyc /usr/lib/python2.4/site-packages/samba/__init__.pyo /usr/lib/python2.4/site-packages/samba/printerdata.pyo /usr/lib/python2.4/site-packages/pygtk.pth
Assuming python-updater forgets about them.
No, python-updater definitely updated them. Please note the pygtk.py is a broken symlink and the samba files are .pyo and .pyc, not .py
It seems to be fixed in last versions of dev-python/pygtk. If you can still reproduce the problem with samba, please file a new bug.