This is the same way my "official version" works. I can remove the serene screen logo from the list, leave nothing but the company logo, but every time the program restarts the serene screen logo is displayed. You have to press the L key each time the program restarts to display the company logo. It is annoying.
What happens if you wait a few seconds after the program restarts?
On my system, when MA3 starts, it displays the splash screen - then the SereneScreen logo for about 10 seconds - and then whatever I have in the list.