It appears that there are several issues with the Navigation Widget in 5.0 SP1. When you have a navigation widget that is triggered from a mashup that has a master(a simple header master is fine) and you navigate with popup, modal popup, or fullscreen, the old master will be on top of the popup or full screened mash-up. This makes the newly navigated mashup impossible to use. This functionality was working fine for us in 5.0.
Steps to reproduce:
Create a 2nd mashup, Test_Nav, that uses Test_Master as its master, and has a single navigation widget. Set the widget to take you to Test_Destination with the FullScreen Target Window Type. (Popup and Modal Popup are also screwed up).
Run the Test_Nav mashup and click the navigation
Create a simple header master , Test_Master, with some different widgets
The window is completely replaced with Test_Nav
A mishmash of the Test_Destination and Test_Master.