I've not done the work around you're asking about but will note the following as it is how I deal with the issue I think you're describing.
The main Nagios display uses frames so the menu you see is in one frame and the main display you see after making a menu choice is in another frame. When you hit refresh it is reloading the main frame (the one with the menu) so goes back to the default.
In IE8 if you right click on the frame you want to refresh and select refresh there rather than choosing the refresh next to the URL bar at top it will refresh that frame. In Firefox if you right click and do "This Frame -->Reload Frame" it will only reload the frame you are in.
If there is something you need to have permanently up (i.e. you don't need the menu frame) what you can do is simply get the URL the menu item points to then use that in your URL bar so rather than showing it as a frame it is showing what was formerly a secondary frame as the main page and no longer showing the menu frame.
For example the menu button "Hosts" may have properties that show its URL is:
If you put that in the URL bar it will ONLY show the Hosts information as main page rather than as a frame next to the Menu.
With tabbed browsing you can simply right click on the items and tell them to open in new tab - that will have the same effect as cutting and pasting the URL.