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 had the same problem some days ago. I found a fix in another question here in stackoverflow, but now I can't find the link.
In Eclipse: right-click on your project > Properties > C/C++ General > Code Analysis > Launching and disable both options ("Run with build" and "Run as you type").
There seems to be a problem with CDT and the Indexer, doing this you hide the problem. The editor will still complain but now you should be able to run and debug your application.