Melodyne works fine for me. Yes... you can not work exclusively in the MD window for setting the playback start point... you must do that from the Sonar time line. And you have to stop the playback to "jump to another section of the since since in playback....MD is following the clock not the time line. As long as you start properly, they stay synced.
For me this is not a problem. I keep the Melo window below the time line and start and stop from cake and it works fine.