ooh! ooh! ooh!! i know the answer, i know, i know!!!
ok, here's the deal. for some odd reason, both games were orginally created with the SAME folder name. so, when you back them up, you get problems.
here's how i fixed my problem:
1. first make sure no other RS3 game is on your box (HDD)
2. copy BA to your box, then change the folder name via ftp and add BLACK ARROW or whatever you want
3. now copy the other RS3 game to your box and both should work fine now
see, i learned this the hard way. apparently alot of the files within the folders of both games have the same names and extenstions. what i did was first copy RS3, and then i turned around a made a back up of Black Arrow. so, when i loaded my game, it gave me the original RS3 splash screen, but it was the Black Arrow dash (main menu). the game still played, but my sounds were all f'd up. i can only assume this is because the original RS3 game and Black Arrow game had the same folder name and file names and extensions. so, with me backing up my BA, some were overwritten.
hope this works for you!