For Google and posterity.
I recently reverted my home machine from Ubuntu 9.04 to 8.04 (long story). I re-used my old Eclipse workspaces, and after getting my Eclipse CDT projects compiling cleanly again, I still had various "include path not found" compiler warnings, referring to now-obsolete and invalid include directories. Eclipse regarded them as 'system' directories so I couldn't manually remove them from projects' path settings.
The culprits were .sc (scanner, I think) files in
.metadata/.plugins/org.eclipse.cdt.make.core. These files, one per project, seem to be cached paths and environment variables used by the build tools. I just closed Eclipse, removed all these .sc files, and they were recreated when I re-opened Eclipse. Problem solved.