One of the cool features in PDE/Build is the generation of source features and plug-ins. This is perhaps one of those features that leads towards the "black magic" reputation that we seem to have.
Recently the CDT SDK builds have been missing their source. The source features and plug-ins exist, but they just didn't contain any src.zips. After some investigation, it seems that a long standing bug in pde.build has risen to the surface. It has always been there, it was just hidden by bug 114150 which was fixed in M6.
The workaround for the CDT is simple: just make sure that in the SDK feature, the generated org.eclipse.cdt.source feature is included after the org.eclipse.cdt feature upon which it is based.
Unfortunately, I'm sure that the fix in pde.build will be a bit harder.