While the root cause of this problem is still unknown to me, after some investigation and with a help from Robotium's author Renas Reda I could confirm what I initially suspected that emulator indeed locks itself.
A workaround I'm using now is this code put in setUp
method:
getInstrumentation().runOnMainSync(new Runnable() {
@Override
public void run() {
getActivity().getWindow().addFlags(WindowManager.LayoutParams.FLAG_DISMISS_KEYGUARD);
}
});