I have experienced this scenario once before and now today, whenever I updated my QGIS installation on Ubuntu, it didn't reload python plugins under ~/.qgis2/python/plugins when started, only c++ plugins are available. I can't really recall what I did previously but when I restarted my machine it seemed to work out of the box. Any ideas?
AndreJ is right. When I did an upgrade of QGIS from version 2.6.0 to 2.6.1, python-qgis was not upgraded in the process and was held back at version 2.6.0. This I confirmed by running dpkg below.
dpkg -s python-qgis
After manually upgrading python-qgis as suggested by AndreJ.
sudo apt-get install python-qgis
QGIS finally was able to reload python plugins.