On my Windows platform, I have the latest version of adt bundle (20140321) and ndk (r9d) installed. The installation is as clean as it gets. The environment variables NDK_ROOT,
I solved this for adt-bundle-windows-x86_64-20140321:
.settings
.classpath
.cproject
.project
project.properties
Also this solved issue with Eclipse 4.3 previously ignored build system and user defined compiler flags. Now macros folding dependent on this flags etc works fine.
If more general - NDK plugin can properly define for you right includes and anything other required to work fine, but you need to clean your project from broken crap.