Google has recently been deploying migration/integration of Google Apps Accounts to work more like a regular Google Account. Nice feature but migration is not as smooth as one would think.
I expected Google to implement a "seamless" migration. That is to say, if I had a Google Account of email@example.com and also Google Apps for domain.tld when Google Apps is expanded data from the general Google Account would be merged/migrated/re-associated - poof. Perhaps even the Google team could have created a conflict-merge tool. Complicated but, they have loads of cash and many intelligent people.
For some of our clients this migration has been not a big deal, perhaps only one or two accounts were even affected. For them the case was easy - turn all features on and for the general Google Account they were simply deleted.
Other accounts needed to pull Calendar and other data to then re-publish in their newly-enabled full-featured Google Apps Account. This is a tedious process.
Delete your old general Google Account account by logging in, by-pass any migration steps and then pick "Manage My Account" and then "Edit" under My products section.
Other users had some accounts that were tied to many, if not most, Google services such as Blogger, Checkout, Picasa, Analytics, Webmaster Tools, YouTube, &c. Here is a BIG ISSUE if you read this help page from Google it will tell you accounts connected to many of those services cannot be migrated - they will continue to work - and hopefully be migrated soon. It may make sense to hold off on migration until the process with these services is worked out.