I like using the the android app instead of a real remote if I'm expecting to use Search to find a movie. The phone's keyboard is so much easier than picking letters one by one with the real remote.
Once I use the android remote, the Roku seems to ignore the real remote. It continues to ignore the real remote for a while (some hours). Eventually I'll try the real remote and discover it's working again.
Has anyone else seen this behavior? Is there a trick or workaround that helps? I'm using a Memorystick+