I am support for a user who has inherited an already configured Acrobat X. This user when applying password protection now gets a second popup asking for "Confirmation of Permissions Password". This apparently is new and only started happening this week. Her complaint is that it doubles the amount of time to protect ECN Documets.
You are always asked to confirm your password a second time. This is to confirm you typed the password you meant to. Otherwise you could encrypt a file without having the correct password.