Sorry for the trouble with this one.
It seems like you have used the new iPhone 6, 7 size in Mockups 3 for Desktop. This new feature is not available yet in myBalsamiq, which is why you see the iPhone size reduced in this case.
You may want to avoid using this iPhone size for now, or at least for projects you wish to move to myBalsamiq. Alternatively, you can use the Full Screen Presentation Mode in Mockups 3 for Desktop or export your project to a PDF to demonstrate your project, your links will still work in both cases.
Hope this helps! The major update that we are preparing for our web version will make all the version 3 goodness available there too.