A bug that I noticed on both iOS and Android (didn't test on other platforms): if you call NativeMessageBox with a callback, the second call with crash as the callback is deleted. This wasn't happning in previous Juce versions.
To fix this on Android I had to remove line 671 of Juce_android_windowsing.cpp:
delete callback;
On iOS, I replaced line 162:
ScopedPointer<ModalComponentManager::Callback> callback;
by
ModalComponentManager::Callback* callback;
Now the crash doesn't occur anymore.