[Zubersoft]

Thank you, I think I see the problem here, but I will have to verify. There are a couple of things I believe are an issue:

1) Annotations are only saved for a given page when changes are detected on that page. Switching a layer on or off is not considered a change and will not cause the save to trigger.
2) Changing pages will save the annotations on that page, but once again, changing the layer visibility will not trigger the save to occur, so if you just change the layer visibility and exit the annotations editor, the layer visibility will be set correctly for that session, but if you restart the app, the layer visibility will be reset to an incorrect state where it may be saved for some pages but not others (depending on whether you had added or modified annotations on those pages)
3) Force killing the app while annotating may result in any changes that were made being lost. So I would not advise doing this during regular use.

I am going to change the application logic so that changing the layer visibility will flag each page containing an identically named layer as needing to be saved. This should fix all the issues you are seeing. 

Thanks,
Mike