Again I just need to say that this is not related to the Dashboard, but how BI Launch Pad renders the dashboard when it displays it. If you save the dashboard out as a flash file and open it outside of BO, it displays correctly without the border.
In regards to the scroll bars, it appears that 4.1 changes how it displays the dashboard and makes the size a bit smaller than it was on 4.0 which means that you have to move all objects a pixel to two so it doesn't go outside. Very annoying and takes a lot of time to clean up.
Cheers,
Josh