Sounds like @Danny is in the same position as me, and many others I know.
Effectively, pre MobileMe/iCloud, we would all use our existing AppleID to purchase apps (a gmail, hotmail or any other email address you had).
Then MobileMe/iCloud came along, and offered the wonderful syncing service, which created a new Apple ID.
For those who hadn’t used their previous ID for many paid purchases, this wasn’t a massive issue, as you could just use the new me.com to re buy, or simply ignore the old purchases.
I had quite a few paid for purchases, so I kept the 2 running side by side, with the assumption that one day you could merge them.
Fast forward to now, and I’d have to spend a ton of money to re-buy the old apps with me me.com Apple ID, so I’m left with 2 running side by side.
It’s not disastrous, as my me.com is my main AppleID when signing into things, but the old AppleID is used for App Store purchases exclusively.
It works, but it’s annoying for anyone who likes to keep things simple.