This feels silly, but its been 2 days...somewhere after upgrading from Ubuntu 10.04 to 10.11 and from Eclipse Helios to Eclipse Indigo, I got stuck with the following problem:>
For me, it was solved by adding a specific ‘Source Location’ folder, and removing the default. In Luna, it is under:
Project > Properties > C/C++ General > Paths and Symbols > Source Location