I have updated my Ubuntu box to 11.10 and then Eclipse also have been updated to 3.7.0 Indigo with CDT 8.0.1
Then the following problem occurs:
In the project properties, go to C/C++ Build > Tool Chain Editor, tick Display compatible toolchains only, and select Linux GCC and click Apply button.
Now if you go to C\C++ General > Paths and Symbols, you will see new list of include paths added. If you rebuild index, the error messages should go away.