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:>
I have experienced similar problems of the CDT reporting errors even though the code compiled fine within Eclipse Indigo.
Project > Properties > Settings > Binary Parsers > "GNU Elf Parser"
helped in my case. I had the "Elf Parser" checked.