Cannot get Media Bay to playback in sync with Cubase Project. “Align beats to project” is selected. Please help!!! 
Have you got any plugins on your master out?
Mediabay playback doesn’t compensate for any latency that builds up on the master and so becomes out of sync - another of those annoying oversights that plagues many half baked features in Cubase.
Turn off any plugins you have there and it will play in sync again.
It’s because you need to make sure the sample in media bay starts on the 1 of a bar. On the first best of the bar. Yiu may have to shift your arrangement forward or backward to make sure it’s aligned correctly.
Use ‘constrain plugin delay compensation’ and it will work fine. Would be great if latency compensation could be incorporated in an update though.