I have an Android NDK project whose NDK part compiles ok from command line;
I used to have no problems with running the compiled stuff from under Eclipse as a pure Java project.
How it can be ignored: open 'Problems' window, select errors in c/c++ files and press Del key. A confirmation msg box will be shown, but after that you can debug your app... until next rebuild =)
Alternatively, as you mentioned earlier, you can just close all opened c/c++ files.