Unity integrated into Native app locks orientation to Landscape

Hello all - we've been producing apps for various companies that have Unity embedded in a native side application. With the latest Unity release 5.5.1 for iOS we've found that after starting Unity it's locking orientation to landscape even after we've requested Unity pause from the native side and the native programme has become dominant over it.

It never use to do this so we figure that there could be a settings option somewhere that we've missed, or an updated file that's defining this behaviour etc. Long story short we're now very behind deadline and getting pretty stressed/irritated about this so any help will be appreciated!