For the "Android OS not ready" issue, if the user close YouWave and does not save the state, upon restarting, the Android will reload and most of the "OS not ready" case will be gone. No need to worry, even if Android is reloaded, the data are still preserved.
For the root issue, yes, we are aware of that even if YouWave is already rooted, some apps that need rooting report that YouWave is not rooted. Can you please let us know the name of this app? Different apps have difference ways for the root check. Obviously the check of your app does not pass on YouWave.