In my android logcat log, I see:
01-02 02:01:46.523 E/ActivityManager( 459): ANR in com.android.phone (com.android.phone/.InCallScreen)
An
I have found this interesting bug report:
http://code.google.com/p/android/issues/detail?id=41755
Short summary is that there seems to be a bug in the NDK wrapper code which means that events coming in from multiple sources can cause an ANR. This precisely matches my use case --- I have an NDK app with work happening in background threads and a gamepad, and the ANR I'm getting precisely matches the one you described and the one in the bug report.
Is this similar to your setup?
Update: more info: http://ps3computing.blogspot.co.uk/2012/12/anr-application-not-responding.html
After having applied the fix described on his blog, I don't seem to be able to make the ANR manifest again. That's not to say it's gone, though...