I've had that same issue. I'm hoping to hear if anyone else has figured out a fix/workaround, but I can tell you what I was told with Apple customer service.
Basically, you can't merge your two accounts into one, which sux, but I think I've heard rumor that someone at Apple said, or someone asked an Apple employee if, there will be a fix for this in the future. Not sure yet.
If you have to keep your original ID and your new ID/email address, you can use both. It is just a little more annoying - but not too much.
You would need to keep both if, as in my case, most if not all of my apps were purchased with my first, original Apple ID. Then after a few years, I decided to use MobileMe. I guess without thinking, I used an email address different from my original Apple ID.
So, to keep apps history and my email account stuff (contacts, calendar, etc), I use my MobileMe (@me.com) address to sign into iCloud. Then, I sign into the App Store with my original Apple ID.
This has solved most of my issues, but now I'm having trouble with the iCloud deleting the documents on all of my synced mobile device even though I created it in iWork from one mobile device. I think there is a slight work around for that, just really sign out of all accounts everywhere possible on mobile devices and on your Mac.
Hope that helps, but I would still like to know if there is another way.