I have a similar problem. I used to own a .mac email address, which I had moved to MobileMe for a while then discontinued. However, I made an Apple ID when I had the .mac email address.
So, I had
firstname.lastname@example.org as my Apple ID.
email@example.com was my old MobileMe ID, which I discontinued.
When I made iCloud ID, it defaulted to:
Problem is that unlike OSX Lion email, I cannot set up iOS 5 email to ignore firstname.lastname@example.org and only use email@example.com! Email is stuck at firstname.lastname@example.org and I am not allowed to send any emails. I can receive emails addressed without any problems, but I cannot send any emails.