Yes this is an known issue Apple is expecting a great number of users to have to do (currently – there is semi-substantiated rumours they are designing a Apple ID merging system; but I'll believe that when I see it).
I (and almost everyone I know) have an issue like this:
Before we signed up to me.com we all had our iTunes Apple ID's. But annoyingly, Apple automatically sets-up a new Apple ID for all me.com email addresses as well. So we all had:
(1) our original Apple ID: "whatever" (usually we used a NON-email address for this, eg. ""firstname.lastname")
Then we went into appleid.apple.com and made the contact email our new me.com address.
(2) then we ALSO had the auto set-up me.com Apple ID, always the full email: eg. firstname.lastname@me.com
We all ignored this Apple ID, and NEVER used it to log into anything Store related (just used for the email/contacts/etc. set-ups).
For this new stuff you should do this:
(3) make sure you use the FULL email (ie. example #2 above) for the set-up and use of your Apple ID for anything "iCloud" related.
(4) make sure you use only the ALIAS part of the email [just the front bit before the @, in my case above] (ie. example #1 above) for the set-up and use of your Apple ID for anything "iTunes" related (basically all the stores, iTunes/Mac App Store).
- on iOS devices go into Settings>Store and log-in using your iTunes Apple ID there.
- on Macs, in iTunes AND the Mac App Store, make sure your logged-in using your iTunes Apple ID there.
So yes, you have to use two Apple ID's (one for iCloud, one for iTunes/MAS) for the moment.
This is annoying as they are (a) forcing you to use TWO Apple ID's, & (b) they are forcing you to use the full email address for your iCloud Apple ID (though perhaps understandable, as everyone is being issued a me.com for the iCloud service, so this may help people to remember the exact email domain address they are using when logging in).
Hope this helps. — well, at least until Apple fix so accounts can be merged in the future sometime, one wonders! ;-)