You can put the script in the Welcome.txt file in language file, I will have to go back and see if I can find the right way do do it in one of my backups. I don't use it anymore, but it took me quite a few tries to figure out the best way to do it..
Michael
edit
I could not find any thing in my back ups, so I'm guessing that I did it the way it shows in the 1st part of this thread in the welcome.tpl file.
I remember putting some graphics in the LBL_Welcome txt file in ACP under language, but not sure on putting Flash file there. this is the way I got a image file to work in the lbl_welcome_txt file.
Code:
img src='/yourlocation/skin1/images/payment_xxxx.gif' /img>
Not sure what you would have to change to get a flash file to work there, or if it even would..
Michael