Link Option
when created a hyperlink for a page view option and selected a page from another pdf and saved, the default option to open the hyperlink when clicked is set to "Windows set by user prefrence". There should be an option to set it to any option available there.
All the other parameters are saved as per the last saved prefrences, only this doesnt change.
Hope you would look in to this and do the needful and its the best PDF software.