A. When you virtualize an application, you want to abstract the application from the underlying OS so certain changes an application makes are captured into per-user/per-application pkg files instead of writing to the normal user file and registry locations. This means that if a user runs both a virtualized version of an application and a locally installed version of the application, they'll get different settings.
The best solution if this is an important concern is to use a technology such as AppSense that virtualizes the user profile at an element level. If you're running local or virtualized applications (and even running the same applications between Windows XP—v1 profiles—and Windows 7 or Windows Vista—v2 profiles) you'll get the same shared profile available and the same application settings. The cool part is that because AppSense treats the profile as separate elements on a per-application level instead of one giant profile, when you open or close applications it syncs those portions of the profile. You can have multiple logons on different OS versions and application combinations and you'll still get the latest settings without logging of or on.
Another option is to use a technology, such as PolicyPak, that also allows the sharing of settings between virtual and locally installed applications.