Until earlier this year, it was possible to have two different accounts, one for Google and one for Google Apps, but both with a login-name of YourName@YourDomain.TLA (or YourDomain.XX.YY or whatever setup your own domain is).
People had the Google Apps account created for them by their domain-administrator and the other got created when they used the same account-name to sign in for Blogger or Picasa (or any of the "older" Google services that weren't part of Apps previously).
To fix this, Google created an account unification process. Under it, the first time that the the Google-account user logged on after their domain had been upgraded to use the full product set, they were told about these conflicting accounts and asked to transfer their existiing content (blogs, photo-albums, etc) to a different Google Account.
Eventually, this process will mean that there are no conflicting accounts left - but this will take a while, because it depends on the owner logging in to a "non-native" apps product. Some of them won't have done so yet, and some never will.
Also, I think there are some remaining differences between Google Accounts and Google Apps accounts, beyond the admin-level service control: for one thing, they have different options available to them then restricting the access to web-pages made with Google Sites. I don't know if this is deliberate or not, or what other implications it may have, but it's something I may be investigating soon.
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