Hi,
First of all i want to tell you whenever you set any default parameters in Backup exec it will reflected only in new jobs not in the previous, so for that you have to set them manually.
Now for encryption key apply issue, please check the followings:
Whether you set the key mode to restricted or common. If you key mode set to restricted then only the user who has created it can only apply it. So if you login on your backup server as a different user, then try login on backup server as a user who has created the key and then apply it. Or else set the key mode to common.