I've dug a little more into the problem. I was able to insert the seal correctly into the "bad" back. It lays there correctly but is not held. So it comes out with any false move. The seal is the correct size so that's not a problem. The channel that holds the seal was damaged a bit in the "good" back. I'll try to clean it up and see if I can make it work. As I intend to use this controller as a backup, I don't really care that much if it's water proof. So if I can't fix the channel on the "good" back, I'll just assemble it without the seal.
Thank you everybody for your help and suggestions.