Ever since apple has decided to make iTunes account access your email address instead of a username I have noticed the apps that were bought under the old username do not recognize this and there doesn't seem to be a simple way to fix this. For example when an app has an update it asks me to enter my old username/pw combo, however if I make a new purchase and then it has an update the new email/pw info is displayed. This more of an inconvenience than anything, but the other day I was trying to make and in-app purchase and the new email/pw dialog displayed for an app I purchased with the username/pw and the transaction would not go through saying I needed to purchase the app first. Is there an easy way to fix this?
Was your old username linked to your current email address?
Supposing the two aren't linked, there isn't an easy way around this, although you might try contacting Apple support to see if they can transfer those purchases to your account. I've had luck doing this before when an album I purchased was link to the wrong account.
Have you tried removing the app from iTunes and and the iOS device and then downloading them again? iTunes should see that you had already bought it and just downloads it.
This way I changed some apps when I got the iOS device from my girlfriend, which were bought with her account.