Hi Entasis, first check out this post:
http://techboard.nemetschek.net/ubbthreads/showflat.php?Number=77492
What exact version of VW are you using. And are you on Windows or Mac?
Your Layer View Settings, under View > Layer Options, should be independent of your Viewports as far as I know. In fact I have a semi-related wishlist item that asks for this situation to be slightly altered:
http://techboard.nemetschek.net/ubbthreads/showflat.php?Number=73194
When you say "open one of my viewports" do you mean you right/ctrl-click on a Viewport and select "Edit Design Layer" or do you double-click a Viewport and then choose Design Layer? Or do you mean something else?