Apple ID's, iPods and combining accounts

Recently bought a new Mac Mini. When I plugged in my iPod it said that it couldn't transfer my apps from iTunes because it didn't recognize the iPod, so I signed in. A few days later I updated my iTunes old e-mail address to my Apple ID, because I no longer use that old e-mail address. I got a confirmation that said it was changed successfully. I thought that was the end of it but then around a week later it said the same thing (that it couldn't transfer my apps from iTunes because it didn't recognize the iPod). I went round and round trying to fix it, and finally ended up calling Apple. They said that my iPod wants to log in to my Apple ID account but it can't because iTunes doesn't recognize Apple ID's. This surprised me. So now, apparently, I have two accounts for iTunes (my old one, which I guess didn't change after all, and my Apple ID account, which Apple claims I can't use). I'd like to combine them into one. Again, according to Apple you cannot do this but that doesn't sound right and I'm hoping that I just talked to a new iTunes phone rep. I mean, why would Apple not allow us to use our Apple ID's and combine two accounts into one account? This doesn't sound right to me.

If anyone knows how to fix this PLEASE post and let me know. I'll try anything...