Andy, sorry to tell you this but the magic 3 doesn't like gta vice city/kingdom hearts and some more games i can't remember. Thats why they have just released the magic 3.1 to sort these issues out.
I've done a post somewhere on this forum labeled magic 3 and 3.1 issues.
Have a look at that.
Problem is, I've seen it happen with the original disks 2
Sorry it's not good info