The problem is that some older older programs, that were designed
with a traditional admin account in mind, will either not
function properly or throw error messages if it cannot access
restricted areas of the OS.
This can usually be overcome by starting and running the program
as administrator, if you decide that it is safe to do so.
The puzzling thing is why 'Run as administrator' is necessary for
the standard user/administrator account set up on installing Vista.
This account surely should be able to elevate its privileges for
operations that require it through the UAC 'Do you want to continue'
dialogs. Why would you need to start the operation using 'Run as
administrator', or indeed do you need to at all?