There's appears to be a problem with the CDT contribution to the Project Explorer when PyDev is enabled (which isn't covered by the previous Project Explorer bug...).
When the 'PyDev Navigator Content' is enabled, the CDT 'Binaries' and 'Includes' containers don't appear in the Project Explorer.
See this image for an example: https://bugs.eclipse.org/bugs/attachment.cgi?id=90488 (compare the C/C++Projects view with the Project Explorer). Disabling the PyDev contribution fixes the problem.
This is using pydev 1.3.15, CDT 4.0.3, Eclipse 3.3.2